I am using the a spesific CNT structure that I created with mathematica as the initial data file. I want to equlibrate it and then freez the edges and later displace the end region atoms to elongate it. I am following this tutorial by simon except that I am not using the CNT created by VMD ( I have my own CNT structure) : https://lammpstutorials.github.io/sphinx/build/html/tutorials/level1/breaking-a-carbon-
nanotube.html
Could you please help me with using the equlibrated CNT as the initial data? How to tell LAMMPS to use the equlibrated CNT as the starting point (to do the rest of simulation on the equlibrarted CNT)?
How about writing out a data file with your equilibrated structure at the end of your equilibration? That you can then use as input geometry in the next run.
I was trying to do that. I got the atoms positions of the equiblirated structure, but its a little bended. I need to add the cross bonds as well which are like this (in the initial structure I had 2 types of bonds, the ones you see in the previous picture and the following bonds):
Since the equlibrated structure is bended a little bit, I find it difficult to add the cross bonds . I was looking for a possible easier way to do this.
This is a discussion you have to have with your adviser. I am not familiar with your research or the tutorial you are referring to. But since you are requiring additional modifications, you have to deal with the consequences of that. Tutorials are meant to give people an introduction into workflows, they are not the final answer to how certain things must be done all the time.
This statement doesn’t quite make sense to me since in LAMMPS (and molecular dynamics in general) you can just add a bond by specifying which two atoms to join. You don’t need their positions. Look at the Bonds section of your data file and you’ll see it’s a list of “bond ID, bond type, bond atom 1, bond atom 2” (and maybe other numbers I can’t remember, but definitely not coordinates).
So it shouldn’t matter that there’s a little wiggle in the nanotube.
