Asking for Suggestions!

LAMMPS
1

Hi,
I am preparing a nanopore model where graphite is used to make two slabs, a bulk region adjacent to that nanopore, a dead-end-wall and a piston like rigid body are also created using the same carbon atoms. Then hexane molecules are inserted inside the bulk region. The expectation is that the piston will push the hexane molecules towards the nanopore. But, after running the model, I have seen that the hexane molecules are not moving and the piston is pushing the molecules to the nanopore, but the liquid molecules are not dynamic. So, now I am seeking some suggestions from your expertise what I have put wrong here for which the hexane molecules are not moving like hydrocarbons. The structure, hexane template and in files are attached for your convenience. Thank you.

Sincerely,
Akash
C6.txt (486 Bytes)
data.graphite (2.2 MB)
input.dat (3.3 KB)
dump_graphite_channel.lammpstrj (5.7 MB)

2

Your chances to get the kind of suggestion you are looking for here are very small. Your question is of the kind “how do I do my research project” and not about LAMMPS itself. People here don’t have the time to first learn the details of your research project, then debug your input and understand whether the problem you are describing is a real problem or just a misinterpretations of the data, experiment with various options to clarify the issue. All of this is a lot of work for people that volunteer their time and have no vested interest in your research project.

There are usually two recurring recommendations given in these cases:

  1. Consult with the people that know and care about your research project, i.e. your adviser, your tutor(s), your colleagues or collaborators.
  2. Instead of simulating the complete complex system, look at the individual components separately and make each work as expected independently. This will be much easier than debugging the entire input. If you are still struggling to make one component work as expected, you can then create a small and easy/fast to run test input deck for just that component and then post it here with a detailed description where LAMMPS does not behave as its documentation says it would. That is much more likely to provide you with specific advice.