Closed qlx17 closed 3 months ago
We don't include anything like :VOID
in the mass list, because some people call it that, others call it :X
, still others might call it :None
, etc. The user should set whichever one of these they intend to use by adding it to the (exported, global) rc
dictionary before calling Molecule
:
rc[:atomic_masses][:VOID] = 0.
Thanks for your explanation. That is a more general way to add custom atomic masses. Perhaps this should be documented in the molecules chapter of the documentation?
Yes, that is a very good idea.
I would like to define a nitrogen molecule with charges derived from the TraPPE force field. In this setup, point charges of -0.482e are placed on the two nitrogen atoms, and to maintain charge neutrality, a point charge of +0.964e is placed at the center of mass of the nitrogen molecule. This dummy site should have zero mass. Here are my atoms.csv and charges.csv files:
atoms.csv
charges.csv
However, when I run
molecule = Molecule("N2")
, I encounter the following error:I believe this error occurs because the atomic mass of VOID is not defined. I suggest adding the atomic mass of VOID as zero to the append_atomic_masses() function so that a more general molecule definition can be supported.