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VlachosGroup / pMuTT

Python Multiscale Thermochemistry Toolbox (pMuTT)
https://vlachosgroup.github.io/pMuTT/
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Calculation of entropy does not include entropy of the elements of the molecule #206

Closed wittregr closed 1 year ago

wittregr commented 1 year ago

Version of pMuTT v 1.3.1

When computing the entropy of a species the entropy of the elements is not included. This results in the incorrect entropy of formation and related thermodynamic quantities of formation relying on entropy. This is the same issue described in more detail in the PythonGroupAdditivty issues database issue 17.

wittregr commented 1 year ago

This issue is correct in stating that entropy, Gibbs, and Helmholtz energies do not include the entropy of the elements in the species and therefore do not represent the energy of formation for that species (The enthalpy of formation is properly computed.). This is generally not an issue since these thermodynamic quantities are used to compute changes in these thermodynamic quantities for reactions where the entropy of the elements is the same on the left and right-hand sides of a reaction and cancel.

Nonetheless, to allow the calculation of energies of formation a new function has been added to compute the entropy of the elements in the species (get_Selements) and a parameter (S_Elements) has been added to get_S, get_SoR, get_G, get_GoRT, get_A, and get_AoRT to allow the inclusion of the entropy of the elements in the calculation. The default value is None.

If S_Elements is net to True, then: S = S - Selements G = deltaH - T(S - Selements) A = deltaU - T(S - Selements)