QuantumATK Forum

NanoLab => Plugin Development => Topic started by: Anders Blom on August 29, 2012, 10:39

Title: Fun with graphene
Post by: Anders Blom on August 29, 2012, 10:39
I have made a collection of 3 useful, fun, cool and hilarious plugins that can be applied to graphene (and in fact any other 2D material) to twist, bend, ripple the structure to create buckled structures, half-wrapped tubes, twisted nanoribbons, etc.

To install, please download the attached zip file, then go to Help>AddOn Manager in VNL and click "Local install" to install the file. You should restart VNL to make the plugin active (unless you haven't yet started the Builder in the current VNL session).

Attached are also some examples of systems you can build with this addon!
Title: Re: Fun with graphene
Post by: ramkrishna on August 30, 2012, 12:07
Dear Sir,
         In case of band structure computation we know that we have to take smallest unit cell to avoid the zone folding (no repetition along C direction). Now, if I want to study the periodic rippled system, then I have to repeat the C direction (at least twice) and then increase the ripple amplitude for quite a bit to visualize the proper ripple. Otherwise in a unit cell, I have to keep the ripple amplitude very small so that the bonds do not break and for that it does not produce a proper rippled system. So, is it possible to find the band structure of a rippled system properly? for that, what will be the unit cell so that I can minimize the zone folding? I mean, can I consider a system as a unit cell which has twice/ thrice repetition along C? really puzzled about this. Please help.

Regards
Ramkrishna   
Title: Re: Fun with graphene
Post by: Anders Blom on August 30, 2012, 13:03
If you create a ripple with a different period (but a multiple of) that of the graphene itself, then this becomes the real period of the system. Also, it is never wrong to compute the band structure etc of a repeated cell, it can just be a little bit harder to view the bands because of the folding, but it doesn't change fundamental properties like the band gap.
Title: Re: Fun with graphene
Post by: ramkrishna on August 30, 2012, 13:56
Dear Sir,
         To create the buckled or rippled system we have to increase the buckled amplitude by Angstrom, but can't understand, what is the amplitude exactly means here? When I am increasing it then with respect to what I am giving the increment?

Regards
Ramkrishna
Title: Re: Fun with graphene
Post by: Anders Blom on August 30, 2012, 13:59
It's the amplitude of the wave. So if you set it to 1 Å then the rippled sheet valleys and ridges will be roughly separated by 2 Å in X.
Title: Re: Fun with graphene
Post by: ramkrishna on August 31, 2012, 07:24
Dear Sir,
         In case of repeated cells (at least 4-5 times) it is possible to get a sine kind wave and then we can say that it is the amplitude of wave but for smaller system, like unit cell ( no repetition or 2 repetition) I am not getting proper sinus-shape wave, then what should be the interpretation of that amplitude? Please help me.

Regards
Ramkrishna

Title: Re: Fun with graphene
Post by: Anders Blom on August 31, 2012, 09:29
The fundamental requirement for a sensible bandstructure calculation is that the structure is completely periodic. So any number of repetitions will be fine. The "buckler" plugin always maintains the periodicity of the system, so any number of periods you choose is also fine. Beyond that, it's really just a matter of what geometry you want to study.

It's difficult to imagine that the period of the ripples in graphene would be of a similar magnitude as the unit cell itself. It that were the case, we would probably not be speaking as much about graphene today as we do. For the most part, graphene stays very flat on length scales up to many repetitions of the unit cell. The amplitude of the ripples depicted in various "artists representations" of buckled graphene is also most likely grossly exaggerated. So if you really want to look at realistically rippled graphene, I would first of all look for real experimental results, and if my suspicion holds (I haven't checked myself, I must admit), the structure to build is 10-10 repetitions with a wave period of 1-4, and an amplitude significantly smaller than 1 Å.

Finally, I would also expect that the ripples have a small effect on many properties (not all, of course). Look for instance at our tutorial (http://quantumwise.com/documents/tutorials/latest/GrapheneExplorer/index.html/chap.twister.html#sect1.twister.conductance) where we show the conductance as function of the twist angle of a graphene nanoribbon - the twist at most affects the Fermi-level transmission by 10%. To me, this indicates that the properties of graphene are not crucially dependent on minor details but rather the overall shape of the graphene, a fact supported also by the ability of simple nearest-neighbor tight-binding models to give very similar results as DFT. I assume that the whole "point" of graphene is the sp2 bonding, and that picture is not really broken when you bend, ripple, maime or otherwise abuse the material. Of course, this only holds to a certain point (once you have bent the graphene into a nanotube, clearly things change) and needs to be studied carefully, but this also means that one has to be careful to set up realistic calculations, else the results become meaningless.
Title: Re: Fun with graphene
Post by: marmotte on September 4, 2012, 16:17
Dear Anders,

I have downloaded the plugin but I couldn't find them in the Builder/Add Custom ! could you please tell me where it is installed ?

Many thanks
Title: Re: Fun with graphene
Post by: Anders Blom on September 5, 2012, 15:36
Downloading is not enough, you also have to install them in VNL, and then restart VNL. See the instructions in my original post. However, the plugins will not appear in the "Add" menu, they will be under "Coordinate Tools".
Title: Re: Fun with graphene
Post by: marmotte on September 25, 2012, 16:06
Dear Anders,

Could you please provide some references of the mathematical formulas that you used for buckling, twisting and also tube wrapper. I'd like to have an estimation of the effect of the parameters such as angles.

Thx
Title: Re: Fun with graphene
Post by: Anders Blom on September 25, 2012, 21:05
I'm glad you think these little scripts are useful!

If you download the zip files and extract them (e.g. by installing them in ATK), you will find that the source code for each plugin is provided, so you can just read there exactly what it does. Hope that's clear enough.

Note that the formulas used in this plugin are just examples of what you can do; they do not constitute any universal definition of the terms "buckle" or "twist" (or to some extent even "wrap").
Title: Re: Fun with graphene
Post by: rruisan on August 24, 2014, 02:13
Dear Anders,

I followed the installation step of the .zip, after installing, I put the unzipped folder in VNL / examples /. After I opened the Virtual Nanolab, directs me to tools-custom-builder, opened the folder FunWithGraph I chose one at random but generates nothing. I would appreciate your guidance!
Title: Re: Fun with graphene
Post by: Anders Blom on August 24, 2014, 19:21
The installation instructions says to use the AddOn Manager, nothing about VNL/examples... And the tools you install are in the Builder, not in the Custom Builder (which is a discontinued tool). Please read the instructions carefully.
Title: Re: Fun with graphene
Post by: rruisan on August 25, 2014, 08:17

Dear Anders,

what happens is that I did not know where it was installed the folder and so I put in examples, but I've seen that has installed this direction (), where I followed the instructions in the beginning of this post. What I still do not see! it's like opening plugins.py as I headed to "Builder- Add", but go the route that I put in (), says error when I want to open some plugins.py. If there is a post that explains me to do, grateful if you tell me please apologize for the inconvenience!



Many thanks!
Title: Re: Fun with graphene
Post by: Anders Blom on August 25, 2014, 11:07
I didn't understand that.
Title: Re: Fun with graphene
Post by: rruisan on August 25, 2014, 19:12
I do not understand, once the zip file in AddOn Manager installed. Being on Builder, where I see the ripples in graphene and other example he gives? Thanks in advance!
Title: Re: Fun with graphene
Post by: Anders Blom on August 25, 2014, 22:02
1. Make a nanoribbon or nanosheet
2. Open Coordinate Tools>Buckler or Twister
3. Change parameters, click buttons
Title: Re: Fun with graphene
Post by: rruisan on August 26, 2014, 18:27
Dear Anders!


Thank you very much for the clear explanation, I thank you, just one last question with this topic, for the ripples in graphene, there any tutorial to tell me how I change the parameters being Coordinate Open Tools> Buckler or Twister.  Thank you very much for the kind patience you have me.
Title: Re: Fun with graphene
Post by: Anders Blom on August 26, 2014, 18:40
How you change the parameters? You type in a new number...
Title: Re: Fun with graphene
Post by: rruisan on August 26, 2014, 18:50
I mean to create ripples values ​​take the amplitude, periodicity or angle or all variables to consider.
Title: Re: Fun with graphene
Post by: Anders Blom on August 26, 2014, 18:55
Yes
Title: Re: Fun with graphene
Post by: rruisan on August 26, 2014, 18:59
What values ​​should I wear for generate the ripples? So that resembles reality! there is a tutorial that explains it, please!
Title: Re: Fun with graphene
Post by: david8 on July 21, 2017, 19:16
Hi Anders,

I have download and installed fun with graphene plugin, but I don't know how activate or use
in VNL 2017.0.
Please, could you explain me how to use it in 2017.0 version?

Thanks,

Kind regards,
Title: Re: Fun with graphene
Post by: Anders Blom on July 21, 2017, 19:21
To activate it, restart VNL. To use it, see the tutorials, the addon installs some new plugins in the Builder, the Twister and Buckler tools.
Title: Re: Fun with graphene
Post by: garnik on October 10, 2017, 11:46
I have made a collection of 3 useful, fun, cool and hilarious plugins that can be applied to graphene (and in fact any other 2D material) to twist, bend, ripple the structure to create buckled structures, half-wrapped tubes, twisted nanoribbons, etc.

To install, please download the attached zip file, then go to Help>AddOn Manager in VNL and click "Local install" to install the file. You should restart VNL to make the plugin active (unless you haven't yet started the Builder in the current VNL session).

Attached are also some examples of systems you can build with this addon!

It's an old topic, but just want to say that this is an awesome job, nice
Title: Re: Fun with graphene
Post by: helenvalley on November 17, 2017, 21:50
I have made a collection of 3 useful, fun, cool and hilarious plugins that can be applied to graphene (and in fact any other 2D material) to twist, bend, ripple the structure to see if phenq is worthwhile (https://theskinnyvibes.com/phenq-reviews-and-results/) create buckled structures, half-wrapped tubes, twisted nanoribbons, etc.

To install, please download the attached zip file,   then go to Help>AddOn Manager in VNL and click "Local install" to install the file. You should restart VNL to make the plugin active (unless you haven't yet started the Builder in the current VNL session).

Attached are also some examples of systems you can build with this addon!
Fun and hilarious plugins? I've found these plugins quite useful for my project work. Installation is easy and it has solved my quite a few problems. I would love to see more plugins like these. Thank you so much for creating these.
Title: Re: Fun with graphene
Post by: Anders Blom on November 18, 2017, 20:40
Thanks for your kind feedback - it was fun to write the plugin, but even better that it's useful!