Simulation not running at all due to a KeyError in library_setup.py

[Pablo-Pomares]

Traceback (most recent call last):
File "../bin/library_setup.py", line 665, in
output_frag.write(' %8.3f %8.3f %8.3f\n' % atom_coords[int(a)])
KeyError: 1

What were you trying to do and what happened instead?

Running the methane nvt example at read the docs. Modified the code to update to the new mbuild and foyer formats, this, however, shouldn't cause any trouble. The simulation didn't run at all.

Please include a code snippet that can be used to reproduce this bug.

As you can see above, it is a key error. It appears to be a problem in the read_pbd() function. I couldn't find a reason as to why it is malfunctioning though, it clearly starts at 1 as shown in line 234. The other possibility is that, for some reason, the conditions aren't met at all, which I don't think is the case.

Please include the following details:

• Operating system and version: Pop!_OS 22.04 LTS
• Cassandra version: 1.3.1
• mosdef_cassandra version: 0.4.0
• mbuild version: 0.17.0
• foyer version: 0.12.1