Embedding CNT on metal slab in LAMMPS

LAMMPS LAMMPS General Discussion
1

Dear all,

I want to prepare a system where I can embed a CNT on a copper slab up to a certain depth, just like in the image. Please what commands are useful in doing this? And is there a LAMMPS example/tutorial on this. I only use LAMMPS to run dynamics so I’m not too familiar with system generation aspect of LAMMPS. Thanks for your help.

Screenshot 2023-09-28 174745
Screenshot 2023-09-28 174745653×515 82.6 KB

2

Don’t worry, there’s honestly not that much to be familiar with. LAMMPS is primarily for running dynamics and doesn’t have much inbuilt system generation tools.

However, if you have pre-equilibrated copper slab and CNT LAMMPS data files, you may be able to start by trying the following approach:

  • read_data to input the copper slab
  • delete_atoms with a suitable region to “cut out” a hole for the CNT
  • change_box to accommodate the CNT
  • read_data ... add yes to add in the CNT

Please note that the “correct” way to do this will be very customized to your system, and so the best way to ask for help will be in the form of “I tried X, which according to the documentation and my inputs A, B and C, should do Y, but then Z happened instead” rather than “how do I do Y”.

3

I would do this the other way around:

  • get a data file for the CNT (there are tools for that). Make sure that it is suitable for the potential you want to use, i.e. with or without a bond topology and with or without charges
  • adjust the box dimensions in the data file as needed (using a text editor)
  • read the data file into LAMMPS with read_data and use the extra keyword to add two atom types (since your image suggests creating a binary alloy
  • define a region for your metal atoms
  • fill the region with atoms using create_atoms using the first additional atom type
  • use the set command to change a fraction of those atoms to the second additional atom type to get your allow
  • define groups for the CNT atoms and the metal atoms for use with the next command
  • use the command delete_atoms with the overlap keyword to remove metal atoms overlapping with CNT atoms.
4

Thanks a lot. I appreciate your suggestion on this and your tip on how best to ask questions.

5

Thanks Axel! I will give this approach a try.