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cmelab / planckton

Reproducible exploration of organic photovoltaic morphology self-assembly using molecular dynamics.
GNU General Public License v3.0
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drop cme_utils as requirement #2

Closed jennyfothergill closed 3 years ago

jennyfothergill commented 4 years ago

we only use cme_utils for:

from cme_utils.manip.ff_from_foyer import set_coeffs which should be replaced by foyer.Forcefield.apply

and from cme_utils.manip.convert_rigid import init_wrapper. Not sure what to do about this one, but it'll need updating I assume.

mikemhenry commented 3 years ago

We talked about init_wrapper on slack but just to document this better, that wrapper is used to make rigid bodies work by allowing users in the hoomdxml to set the rigid body id. It has a few limitations, the most annoying one is that all unique rigid bodies must have the same orientation, which is why when we use packmol, we fix the molecule orientations.