Replace unyt.amu with Unit("amu") to perserve mass values from mBuild

[chrisjonesBSU]

This is a quick PR that changes how we use amu units from Unyt. There is some inconsistent behavior with how Unyt handles amu specifically compared to other units. See the issue here

In from_mbuild I believe the goal is to copy over the particle mass as is, but to add on amu units since mBuild uses amu for mass. But, when we do this using u.amu we end up converting the mass to kg. This happens because u.amu is already a unyt_quantity that is in kg. In the issue, there is a suggestion to use Unit('amu') instead.

Example: You can see u.amu does not have the same behavior as u.g or u.g/u.mol, but Unit("amu") does.

>>> import unyt as u
>>> from unyt import Unit
>>> u.amu.units
kg
>>> u.amu
unyt_quantity(1.66053892e-27, 'kg')
>>> Unit("amu")
amu
>>> u.g
g
>>> u.g/u.mol
g/mol

Here is what the change would look like in gmso. IMO, keeping the mass values the same as they are in mBuild, and actually using units of amu instead of kg is preferable.

Code snippet:

>>> import gmso
>>> import mbuild as mb
>>> from gmso.external import from_mbuild
>>> methane = mb.load("C", smiles=True)
>>> top = from_mbuild(methane)

Using unyt.amu (current behavior):

>>> for p in methane:
...     print(p.mass) 
12.011
1.008
1.008
1.008
1.008

>>> for site in top.sites:
...     print(site.mass)
... 
1.9944732980130996e-26 kg
1.673823232368e-27 kg
1.673823232368e-27 kg
1.673823232368e-27 kg
1.673823232368e-27 kg

Using Unit("amu"):

>>> for p in methane:
...     print(p.mass) 
12.011
1.008
1.008
1.008
1.008

>>> for site in top.sites:
...     print(site.mass)
... 
12.011 amu
1.008 amu
1.008 amu
1.008 amu
1.008 amu
>>> 

[codecov]

Codecov Report

Patch coverage: 100.00% and no project coverage change.

Comparison is base (5f98454) 92.07% compared to head (3ffbfcb) 92.07%.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #759   +/-   ##
=======================================
  Coverage   92.07%   92.07%           
=======================================
  Files          67       67           
  Lines        6892     6893    +1     
=======================================
+ Hits         6346     6347    +1     
  Misses        546      546           

Files Changed	Coverage Δ
gmso/external/convert_mbuild.py	93.75% <100.00%> (+0.03%)	⬆️

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[daico007]

LGTM!