Description

We should come up with a unified way of specifying an attribute's dimension. I favor the (units: [mass] [length]^2 [time]^-2) format, with the base units being mass, time, length, temperature, charge, etc.

Motivation and context

It helps to be consistent in documentation and currently we are not.

Is your feature request related to a problem? Please describe.
Some, likely many, I/O operations work on path strings but not pathlib.Path objects.

>>> from openforcefield.topology import Molecule
>>> from pathlib import Path
>>> Molecule.from_file('mol.sdf', file_format='sdf')
Molecule with name '' and SMILES '[H]C([H])([H])C([H])([H])O[H]'
>>> Molecule.from_file(Path('

In #672 and #624, we discussed how the Steinhardt order parameter treats particles with zero neighbors. Steinhardt assigns a value of NaN. We need to check to see how other methods (Hexatic, Translational, SolidLiquid, LocalDescriptors) handle cases with zero neighbors.

The follow-up PR would basically be to review freud for other methods where this problem could arise and copy over the tes

This is very similar to the changes made in #463

From what I understand, the idea in #463, is that for the sake of consistency, the units used by the reference value parameters in write_hoomdxml should be same units that are used in mbuild and foyer (nm, kJ/mol, amu).

Since parmed is actually being used behind the scenes, the reference values are converted from nm and kJ/mol

This issue is a roadmap for Molly.jl development. Feel free to discuss things here or submit a PR. Bear in mind that significant refactoring will probably occur as the package develops.

Low hanging fruit

Want to get involved? These issues might be the place to start:

• Speedups to the code. Both on the level of individual functions and the overall algorithm. [Getting there]
• Look over