Dear LAMMPS users,
Is there a way to access a list of all bonds in a system via some python API, be it lammps.py or PyLammps?
My goal is to define angle potential terms between these bonds, since it looks like there’s no automated way to do that (create_bonds many
only creates bonds and angle terms must be added one by one, as I understand from the documentation)
For context:
I’m building a coarse-grained structure for graphene consisting in a triangular lattice with one particle/bead in the basis, with bonds and angles defined between first neighbors. I currently set up the lattice, add atoms via the create_atoms
command and then run create_bonds many
to. well, create many bonds.
The create_bonds many
command correctly creates six bonds per particle, but no angles, which is expected, according to the docs. I made a Python script that reads the bonds from a data file and generates a sequence of appropriate create bonds single/angle
commands. So in order to have a full system setup, for each lattice/supercell, I currently have to:
- set up the
lattice
andcreate_box
-
create_atoms
in that box create_bonds
-
write_data
to a file - read this file with a python script to generate a list of angles
-
include
the file created by the python script.
I wish to avoid generating and reading/parsing the data file and creating/including the command file for each supercell.
Thanks form an unusually cloudy and rainy Natal,