Thanks for the detailed response. To provide some more context, basically what I am asking is whether the nanowire set up will get me in trouble below due to the fact I am using box units and 160A (the periodic length in this case) is not divisible by 4.065.
Based on your response there may be some overlapped atoms on the edges. However when plotting the stress strain curve I don’t get any overly high stresses or simulation crashing. It looks pretty good to be honest. Is it possible that because I equilibrate (using an NPT) before straining the length is allowed to contract/expand to whatever natural length it wants/should be?
I assume if atoms were overlapped it would crash?
Perhaps the atoms in your system do not overlap because you have not created as many atoms as you thought you did. Presumably, that’s not what you want either.
Unfortunately, I am not familiar with the “lattice” or “create_atoms” commands in LAMMPS, so I can’t help you with your input script.
I can offer some advice: You need to look at your system. Since your system lacks bonds, I would recommend using OVITO (https://www.ovito.org) to visualize your system. Run a short simulation in LAMMPS, and load the dump file using OVITO. (You can also use VMD, but you must create a “data” file first.)
— data files —
VMD (and topotools) can also be used to visualize your system. However, to do that, you must create a LAMMPS “DATA” file. One way to create a data file is using the “write_data” command (from within LAMMPS):
Once you have a DATA file, you can visualize it using VMD using these instructions:
(To visualize the size of the periodic box and check for atom overlap, scroll down to the bottom of that file for instructions.)
P.S. Data files give you more freedom to customize your system. There are a variety of data file builders (a.k.a. “molecule builders”) here. For your simple system, I would recommend topotools or moltemplate.
You can also create a data file yourself (manually). The file format is not that complicated and is explained here