Use list to store compound.children

[daico007]

PR Summary:

After the discussion with @chrisiacovella, we have decided it would be faster to store Compound.children with list instead of the in house OrderedSet. The replacement will speed up both the Compound.add step by removing the comparing stage when adding new children to a set, and the indexing (getting element from a list/set by index). We realized the latter was the cause for #1114, not directly the Compound.add_bond itself, but how the particle is retrieved from Compound.children to perform the addition.

PR Checklist

---

• Includes appropriate unit test(s)
• Appropriate docstring(s) are added/updated
• Code is (approximately) PEP8 compliant
• Issue(s) raised/addressed?

[daico007]

@chrisiacovella, I kept the containment intact, since it's still being used by the polymer.build, and if it's false, the children is not being added anyway. The in-house OrderedSet is kept since we are still using it in the lammpsdata.py, and it's technically a modified OrderedSet with some extra property.

[codecov]

Codecov Report

Patch coverage: 100.00% and project coverage change: -0.02 ⚠️

Comparison is base (87edc4a) 87.15% compared to head (acabea0) 87.13%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1121      +/-   ##
==========================================
- Coverage   87.15%   87.13%   -0.02%     
==========================================
  Files          62       62              
  Lines        6422     6420       -2     
==========================================
- Hits         5597     5594       -3     
- Misses        825      826       +1     

Impacted Files	Coverage Δ
mbuild/coarse_graining.py	92.30% <100.00%> (-0.07%)	⬇️
mbuild/compound.py	97.11% <100.00%> (-0.01%)	⬇️

... and 1 file with indirect coverage changes

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[chrisiacovella]

This looks good!