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Implement basic thermochemistry contributions #5

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schneiderfelipe opened this issue Apr 14, 2020 · 3 comments
Closed
16 of 17 tasks

Implement basic thermochemistry contributions #5

schneiderfelipe opened this issue Apr 14, 2020 · 3 comments
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enhancement New feature or request
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@schneiderfelipe
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schneiderfelipe commented Apr 14, 2020

The following is a brief, cascading outline of all contributions to thermochemistry:

  • G = H - T * S
    • H = U + kB * T
      • U = E(el) + E(ZPE) + E(vib) + E(rot) + E(trans)
    • S = S(el) + S(vib) + S(rot) + S(trans)

Above I use the following definitions:

  • E(el) is the total electronic energy [equals E(kin-el) + E(nuc-el) + E(el-el) + E(nuc-nuc)]
  • S(el) is the electronic entropy
  • E(ZPE) is the zero temperature vibrational energy
  • E(vib) is the finite temperature correction to E(ZPE) due to populated excited vibrational states
  • S(vib) is the vibrational entropy
  • E(rot) is the rotational thermal energy
  • S(rot) is the rotational entropy
  • E(trans) is the translational thermal energy
  • S(trans) is the translational entropy

All values incorporated into G, H, and S will be calculated using the following models:

For some information on how RRHO is implemented in some codes, see here, here and here. All this should be organized in a proper module. Ideas for names: thermo, thermostat, mechstat, rovib, rovibs.

Collateral features

This scheme will allow us to

  • calculate all values above for any temperature
  • calculate all values above for any isotope substitution
@schneiderfelipe schneiderfelipe added the enhancement New feature or request label Apr 14, 2020
@schneiderfelipe schneiderfelipe added this to the 1.0 milestone Apr 14, 2020
@schneiderfelipe schneiderfelipe self-assigned this Apr 14, 2020
@schneiderfelipe schneiderfelipe added this to To do in First publication via automation Apr 14, 2020
@schneiderfelipe schneiderfelipe added this to To do in Thermochemistry via automation Apr 20, 2020
@schneiderfelipe schneiderfelipe moved this from To do to In progress in First publication May 28, 2020
@schneiderfelipe schneiderfelipe moved this from To do to In progress in Thermochemistry May 28, 2020
@schneiderfelipe schneiderfelipe pinned this issue Jul 4, 2020
@schneiderfelipe
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Discussions about kinetic isotope effects were moved to milestone 1.1.

@schneiderfelipe
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Discussions about kinetic isotope effects were moved to milestone 1.1.

This is not related to kinetic isotope effects, so keep it in 1.0.

@schneiderfelipe
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Discussions about kinetic isotope effects were moved to milestone 1.1.

I'll close this despite the points on kinetic isotope effects, which is not the priority right now. Issues #10 and #24 currently deal with the challenges of automatically calculating and simulating for any isotope substitution.

First publication automation moved this from In progress to Done Nov 23, 2020
Thermochemistry automation moved this from In progress to Done Nov 23, 2020
@schneiderfelipe schneiderfelipe unpinned this issue Nov 23, 2020
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