Hi all,
I need to create a CNT polyethylene model in Material Studio. I start with a periodic armchair CNT, create a supercell in z direction. Then I create a repeating unit of ethylene. Using Build polymer, homopolymer package I create a chain of polyethylene. Now I create an isosurface around the cnt and using Amorphous package I pack the polymer outside cnt. But when I pack the polymer outside the cnt some polymer chains come outside the box boundary. Is there any way to avoid that. Or is there any way to delete atoms which are outside the boundary or on the boundary in Material Studio. I have attached a picture of the model I have created.
Dear Abhiram Br,
The amorphous cell is periodic in each direction. The materials coming out from one side gets in from the opposite side.
If you want to view this just go to Display style->Lattice-> Style-> Incell. So you don't need to delete the atoms which are outside the boundary. If you want to avoid the edge effects then increase the cell dimension using the Rubild crystal option.
Sushanta Sethi thanks a lot for your reply.
Actually I was trying to create a lammps data file from this nanocomposite model using msi2lmp tool. Incell doesn't work for that case. I have checked that. However I haven't tried Rebuild option. The main issue is that I need periodic in x and y direction and non periodic in z direction. I believe amorphous cell module doesn't have non periodic in one direction and periodic in other two directions.
Abhiram Br there is no such option to remove periodicity in any particular direction using MS. After you convert into lammps compatible file I think you can convert one direction into non-periodic in your input script.
However, what we do in MS to remove the periodicity in z-axis we simply add a vacuum of nearly 100 Angstrom, so that it could not interact with its image in that specific direction.
Sushanta Sethi Thanks again
I have tried using the way which you have mentioned, ie converting periodic to non periodic in lammps input script. However it's not a good way to perform the simulation as suggested in lammps forum. One another way is to edit the periodic data file to non periodic data file which I am working on right now.
It would be great if you could mention how to add vacuum in MS so that I can avoid periodic effect in z direction.
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