bond dissociation energies for surface bonds

[davidfarinajr]

Motivation or Problem

Bond dissociation energies (bdes) are needed for surface bonds in order to fit BM rules during automated tree gen. However, we cannot currently get bdes for X-A (surface_site - adsorbate) bonds

Description of Changes

Added 2 new Bond methods (add_van_der_waals_bond and is_surface_bond) and modified the get_bde method to use provided metal (default Pt111) to estimate the bdes based on the metal's atomic binding energies from the surface metal library.

Testing

Added a couple unit tests and tested getting bdes for adsorbates in jupyter notebook. Have not tried generating trees yet

[codecov[bot]]

Codecov Report

Merging #2154 (166e102) into master (9534d75) will increase coverage by 0.67%. The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #2154      +/-   ##
==========================================
+ Coverage   47.23%   47.91%   +0.67%     
==========================================
  Files          89      101      +12     
  Lines       24169    26895    +2726     
  Branches     6309     6875     +566     
==========================================
+ Hits        11417    12887    +1470     
- Misses      11539    12660    +1121     
- Partials     1213     1348     +135     

Impacted Files	Coverage Δ
arkane/kinetics.py	12.24% <0.00%> (ø)
arkane/input.py	64.03% <0.00%> (ø)
rmgpy/transport.py	89.36% <0.00%> (ø)
arkane/common.py	76.65% <0.00%> (ø)
rmgpy/kinetics/__init__.py	100.00% <0.00%> (ø)
arkane/pdep.py	25.33% <0.00%> (ø)
arkane/statmech.py	56.63% <0.00%> (ø)
arkane/main.py	19.49% <0.00%> (ø)
arkane/__init__.py	58.73% <0.00%> (ø)
arkane/exceptions.py	90.12% <0.00%> (ø)
... and 4 more

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[davidfarinajr]

Looking good so far. Made a few comments.

Thanks Richard. I'll make some changes to address those comments

[github-actions[bot]]

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