About the material structure in the LAMMPS process


I’m ressearching the nanostructure of 2D materials throug in situ transmission electron microscopy.
Currently, an interesting structure came out while performing the in situ nanomehcanical testing on a two-dimensional material inside TEM, and I am trying to reproduce the interesting structure through LAMMPS.

Since I’m a beginner here, I’ll write down some questions I’ve been curious about.

Question 1.
There is a deformed structure during the dump process running LAMMPS. Can I directly use the positions of these elements? Or do I have to calculate the energy-stabilized state once more?

Question 2.
Usually, tension and compression are used in LAMMPS, but in my case, I want to see the deformed structure after compression and decompression. In LAMMPS, is it possible to give the direction of the force once, change it, and then give the other direction again? Or do I have to run the simulation 2 separately in a format that compresses once and pulls the result?

The first two questions are too basic, so I don’t know if this post fits. As a user who still needs a lot of help, there are many things I don’t know.


It is very difficult to answer your questions because there is a lot of context missing and due to your lack of experience with how MD simulations or similar calculations work. Yet your questions are rather specific for your research project.

If you do want to learn doing MD and computer simulations, you have to start at a much more basic level and then work your way up until you have accumulated the skills necessary to plan, perform, analyze, and interpret your calculations correctly. That, however, is quite a tall order and will take a lot of time. Most importantly, it is near impossible to learn this through online resources and asking questions in a forum. You will need some in-person tutoring and supervision.

The alternative to doing this yourself is finding yourself a collaborator that has the experience that you are currently do not possess. That is usually the path more likely to succeed.

Yes absolutely, LAMMPS allows one to write consecutive runs with different conditions, all within the same input file. Simon