Hi all,
I’m using the bond/create command and I wasn’t able to find this in the LAMMPS documentation, but is there a way to have LAMMPS to dump the atom indices of only the new bonds created as the simulation is running?
Thanks!
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Not directly, but you can do it with some processing of data that is accessible.
You can use compute property/local to dump bonds and their types and bond atoms. If you use different bond types for newly created bonds (they can use the same parameters for existing bond types, if needed), then those new bonds are easy to identify.
Or there is the gather_bonds() function in the LAMMPS python module, which provides access to the global list of bonds and then can be processed in memory in the same way.
Thanks for your reply. I’m looking to collate a list of new bonds that would be in the sequential order in which they were created. If I used compute property/local, I believe I would have to dump really frequently and then use post-processing to create that list.
If you want that specific kind of information in that way, I don’t see much of an alternative to creating an customized version of the C++ code, where that information is readily available.
It may be possible to do a similar thing though using the python module and fix python/invoke, but that requires some creative programming, I suspect.
That makes sense. Thanks!