Dear LAMMPS users,
I am a first year Master student in Material Science and Engineering. I have been recently introduced to LAMMPS and I am currently working on a project to simulate a multi-layered system consisting of alternating layers of CuZr glass and CuZr crystal.
I have separatedly simulated the CuZr crystal layer and CuZr glass layer in LAMMPS. I used Ovito to stack them on top of each other while maintaining some distance between them. I have uploaded an image of the bilayer that I created using Ovito.
I exported this file from Ovito to LAMMPS. Now I want to run a simulation in LAMMPS to equilibrate this structure so that the bilayer is formed.
My question is, is this approach correct? I have been trying to run the simulation in LAMMPS but it is not working somehow.
I would be very grateful if someone could tell me if our approach is correct or not or if there is any other way to create the crystalline-glass bilayer.
Wish you all a great day.
Best regards,
Mahima
I would say that your method for creating a configuration for the system you are trying to study is valid. The thing is that since the merging of the two phases was “artificially” created, the spacing between the phases should be unrealistic and thus might generate some numerical instabilities during the dynamics within the scope of the force field you are using (i.e. forces experienced are bogus). Besides, within my understanding of the approach you used to generate a configuration for each phase individually, the atoms in the glass phase would be expecting other atoms of the glass phase as ghost images (within the periodic boundary condition approach). Same holds for the crystalline phase. Since this is not the case, there might be some unrealistic forces being experienced by the surface atoms in the beginning of the simulation. An alternative for these problems would be to do some dynamics at a smaller timesteps until equilibrium positions that are more rightful in the context of the bilayer system are achieved. But another thing you should ask yourself is whether the force field you are using is suitable for modelling the interactions of this composite system.
Other than that, sharing your input script might help us help you better. However, I would honestly not hesitate to ask help from your supervisor - especially given that you are a Master student, it is quite reasonable to ask help for this.
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Mahima,
your intentions are honorable, but this is not how online forums work. What you are asking is in essence, that forum members become your co-advisers. That is not going to work.
Simply put, requests like “please review my input and tell me what I should do differently” are far beyond the scope of an online forum and rather something you need to discuss with your adviser or tutor; that is their job. The same applies for general questions about how to organize and set up your simulations. That is something to discuss with the people that know about your project. People here have very different backgrounds and are not familiar with the details of your goals (and also usually have no interest in it).
What is on-topic are questions about specific commands that are not answered in the documentation or the referenced publications or when LAMMPS is not behaving as documented.
Also, when you get unexpected results, you can describe the commands you used and the results you expected and why you expected those and the results you got instead.
We understand your frustrations of having to do a complex task and struggling to to stay on top of it. Essentially, everybody has to go through that phase. The way to deal with it is to first practice with simpler problems (e.g. work though available tutorials) until you are confident that you can make meaningful choices yourself and understand why you make them. You cannot write in a paper that you did things in a certain way because some “folks on the internet told you so”, but you have to justify it on your own. That is a normal part of the process to become a scientist.
Finally, keep in mind that people here volunteer their time, so you would want to be reasonable in how much time it will take to answer your questions. If you ask people to do things that will take a lot of time (remember, when people are not familiar with your research topic, they will first have to familiarize themselves with it, which takes extra time) you are taking away time from answering other questions and helping other people.
Regards,
Axel.
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