How to do a carbon nanotube attached in a graphene sheet?



  • Searching in your SAMSON Elements page I noticed some models that would be helpful for what I needing. Said models are from this link: SAMSON Format Exporter
    May please I ask help for how to do those models in SAMSON? I really tried several things and installed a few elements, although I’m nowhere near as the images that I’m attaching. Also I’m planning to do a webinar in computational models for materials science and I was thinking in using SAMSON as my main tool, in the subjects of aluminum batteries and the intercalation of AlCl4 ion. Maybe of some protein and carbon nanotubes. Any help would be very appreciated.

    Thanks,

    Kevin Hidalgo

    1_1600383153257_model. format exporter.png 0_1600383153251_model format exporter.png



  • Dear @Kevin-3 ,

    Thank you for posting this question here.

    To create such a model you will need to have the Brenner interaction model. It is a paid element, but there is a free trial available and special prices for Academia.

    You can check out the SAMSON Tutorials - Essentials 18 - Interactive simulation video that explains how to perform interactive simulations in SAMSON. This video is for an older version of SAMSON, but it should be helpful. To create a model that you attached you would need to create a graphene sheet and then place a nanotube of the desired radius perpendicular to it (you can move, rotate objects using Move editors in SAMSON) and connect them using the same approach as described in the video. So the pipeline would look like this:
    -1- Add graphene sheet and nanotube. You can first add a nanotube using the Nanotube creator GUI - this will allow for precise positioning and size - and then placing a graphene sheet. You may also place them using Move editors in the arrangement close to the desired structure. You can use the Viewport compass to rotate the view by precisely 90 degrees and the Zoom to fit to center the model in the viewport (Ctrl+Shift+Space, Shift+Space).
    0_1600414960206_Nanotube-creator.png
    0_1600415456217_nanotube-adding-graphene-2.gif
    0_1600415696861_nanotube-moving-graphene-sheet.gif

    -2- You can remove some atoms from the graphene sheet in the place of the desired connection to facilitate this connection in the following simulation step.
    0_1600415923981_nanotube-graphene-hole.png

    -3- Add a simulator (Ctrl+Shift+M, or Home > Add simulator). Set the Brenner interaction model as an interaction model, set Interaction modeling as a state updater. Increase the state updater's step size to e.g. 0.5 fs.
    0_1600414841912_Add-Brenner-interaction-model.png

    -4- Start the interactive simulation by clicking Space or Home > Start simulation.

    -5- You can select the nanotube in the Document view and move it using Move editors closer to the graphene sheet for bonds to be automatically created between them thanks to the simulator. Else you might need to help to connect them by hand as shown in the video above using Select (shortcut: R) and Move atoms (shortcut: D) editors or Add editor (shortcut: A) (it's Carbon by default).

    You can also check the SAMSON User guide - Modeling and Simulation on how to perform simulations in SAMSON.



  • Alternatively, you can do this without the Brenner interaction model but with the built-in minimization which uses the Universal Force Field (UFF) and the Add editor (shortcut: A) (it's Carbon by default).

    First, you will need to modify SAMSON preferences (Ctrl+K):
    -1- For the Add editor, disable the "Adjust hydrogens ..." option.
    0_1600418725406_Preferences-Add-no-adjust-H.png

    -2- For the Minimization, disable the "Warn me when hydrogens appear to be missing" warning to prevent it from poping-up on each new bond connection.
    0_1600418739623_Preferences-Minimize-no-H-warning.png

    Then you can apply the minimization: Home >Simulate > Minimize. Start connecting atoms in the nanotube and the graphene sheet using the Add editor (A) - to create a bond simply connect two atoms with this editor.


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