I’ve seen in the help pages for airebo for example, and in many archived messages that bonds are not explicitly included in input files with this pair_style with bond_style, bond_coeff, etc. However, in many visualizations of lammps simulations, especially in carbon nanotubes, which I’m especially interested in, they (bonds) are present.
My question is, is one of the usual practices is to implement these bonds after the completed simulation, by VMD for example?
Thanks,
Guidance welcomed,
dc
I've seen in the help pages for airebo for example, and in many archived
messages that bonds are not explicitly included in input files with this
pair_style with bond_style, bond_coeff, etc. However, in many
visualizations of lammps simulations, especially in carbon nanotubes, which
I'm especially interested in, they (bonds) are present.
My question is, is one of the usual practices is to implement these bonds
after the completed simulation, by VMD for example?
since those bonds are usually gradually turned
on and off, it is not always obvious (same as
in quantum chemistry) when something exactly
something changes from being bonded to being
not bonded or the other way around. it is common
practice in quantum chemistry to just use some
simple distance criterion.
in VMD you can use a DynamicBonds
representation that uses a distance cutoff.
axel.