Thermochemistry for surface species needs correction to account for adsorption/desorption

[cfgoldsmith]

Right now we estimate the enthalpy, entropy, and heat capacity of adsorbates by removing them from the surface and them using the gas-phase counterparts. We can still use this approach, but we need to include a correction for the difference between the gas-phase and surface species:
H_adsorbate = H_gas-phase + Delta H_absorption,
where (trivially)
Delta H_adsorption = H_adsorbate - H_gas-phase

[cfgoldsmith]

We can approximate Delta H_adsorption by assuming that the 3N-6 internal degrees of freedom for the gas-phase species are conserved, and that the only relevant change is the loss of 3 translational and 3 rotational d.o.f. and the gain of 6 new vibrational modes.
I have calculated this correction for H, S, and Cp(T) for 13 different groups
(it seems that .py is not allowed as a filetype?!)

[cfgoldsmith]

We have a generic correction (all for nickel):

1. generic hydrocarbon triple-bonded to surface through carbon: CR*
2. generic hydrocarbon double-bonded to surface through carbon: CR2*
3. generic hydrocarbon single-bonded to surface through carbon: CR3*
4. generic hydrocarbon physisorbed to surface through carbon: CR4*
5. generic hydrocarbon physisorbed to surface through oxygen: R2O*
6. generic hydrocarbon disigma-bonded to surface through carbon and either carbon or oxygen: RCR*
   the carbon is double bonded to the surface, so di-sigma is a bit of a misnomer...
7. generic hydrocarbon triple-bonded to surface through carbon, with an oxygen bond: COR*
   (note that 7. is a subset of 1.)
8. generic hydrocarbon disigma-bonded to surface through carbon and either carbon or oxygen: RCR*
   unlike 6, here the carbon is single-bonded to the surface
9. generic hydrocarbon double-bonded to surface through carbon, with an oxygen bond: CROR*
   (note that 9. is a subset of 2.)
10. generic hydrocarbon single-bonded to surface through oxygen: CR3O*
11. generic hydrocarbon single-bonded to surface through carbon, with an oxygen bond: CR2OR*
    (note that 11. is a subset of 3.)
12. generic hydrocarbon physisorbed to surface through oxygen: CR3OR*
13. generic hydrocarbon disigma-bonded to surface through carbon and either carbon or oxygen, with an oxygen bond: ROCR*
    (note that 13. is a subset of 6.)

[cfgoldsmith]

The data for these 13 corrections are in:
RMG-database/input/thermo/libraries/surfaceThermoCorrections.py