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cfgoldsmith / RMG-Py

Python version of the amazing Reaction Mechanism Generator (RMG).
http://reactionmechanismgenerator.github.io/RMG-Py/
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X in vdW complex gets typed as Xv (vacant) not Xo (occupied) #58

Open mazeau opened 5 years ago

mazeau commented 5 years ago

To get all the database tests to pass, we had to change the adj list for surface dissociation vdW from Xo to X because making a sample molecule would always return Xv and the test would fail.

rwest commented 5 years ago

Probably van-der-Waals sites should be not vacant. They should be occupied.

We're not quite sure what impact it has. Maybe other reactions that depend on the concentration of vacant sites would be too fast if we over-count vacant sites.

So this should be fixed

alongd commented 5 years ago

I think we should add in atomType actions Xo to Xo.breakBond, to have: atomTypes['Xo' ].setActions(incrementBond=['Xo'], decrementBond=['Xo'], formBond=['Xo'], breakBond=['Xv', 'Xo'],

alongd commented 5 years ago

I just learned that a VDW-bonded X site has atomType Xv (not Xo). I'm taking back the previous suggestion, and changing the set action of Xo so it's not allowed to form bonds: atomTypes['Xo' ].setActions(incrementBond=['Xo'], decrementBond=['Xo'], formBond=[], breakBond=['Xv'],