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Update atom enthalpies for H, C, N, O, F, Cl, Br, I with data from ATcT #416

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Update atom enthalpies for H, C, N, O, F, Cl, Br, I with data from ATcT #416

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fcd82ea
Update atom enthalpies for H, C, N, O, F, Cl, Br, I with data from ATcT
May 15, 2020
dae6851
Update ATcT to 1.122r
amarkpayne Oct 18, 2021
3dd4b92
Temp: Use Py branch for tests
amarkpayne Oct 18, 2021
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2 changes: 1 addition & 1 deletion .github/workflows/CI.yml
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Expand Up @@ -8,7 +8,7 @@ jobs:
strategy:
max-parallel: 5
env: # update this if needed to match a pull request on the RMG-database
RMG_PY_BRANCH: main
RMG_PY_BRANCH: update_atom_enthalpies
defaults:
run:
shell: bash -l {0}
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26 changes: 12 additions & 14 deletions input/quantum_corrections/data.py
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Expand Up @@ -34,31 +34,29 @@

# Atom energy corrections to reach gas-phase reference state
# Experimental enthalpy of formation at 0 K, 1 bar for gas phase
# See Gaussian thermo whitepaper at http://gaussian.com/thermo/
# Note: These values are relatively old and some improvement may be possible by using newer values
# (particularly for carbon).
# However, care should be taken to ensure that they are compatible with the BAC values (if BACs are used)
# Data from the Active Thermochemical Tables (version 1.122r)
# Care should be taken that these values are compatible with the BAC values (if BACs are used)
# He, Ne, K, Ca, Ti, Cu, Zn, Ge, Br, Kr, Rb, Ag, Cd, Sn, I, Xe, Cs, Hg, and Pb are taken from CODATA
# Codata: Cox, J. D., Wagman, D. D., and Medvedev, V. A., CODATA Key Values for Thermodynamics, Hemisphere
# Publishing Corp., New York, 1989. (http://www.science.uwaterloo.ca/~cchieh/cact/tools/thermodata.html)

atom_hf = {'H': 51.63, 'He': -1.481,
'Li': 37.69, 'Be': 76.48, 'B': 136.2, 'C': 169.98, 'N': 112.53, 'O': 58.99, 'F': 18.47, 'Ne': -1.481,
'Na': 25.69, 'Mg': 34.87, 'Al': 78.23, 'Si': 106.6, 'P': 75.42, 'S': 65.66, 'Cl': 28.59,
'K': 36.841, 'Ca': 41.014, 'Ti': 111.2, 'Cu': 79.16, 'Zn': 29.685, 'Ge': 87.1, 'Br': 25.26,
atom_hf = {'H': 51.6334, 'He': -1.481,
'Li': 37.69, 'Be': 76.48, 'B': 136.2, 'C': 170.028, 'N': 112.471, 'O': 58.9971, 'F': 18.465, 'Ne': -1.481,
'Na': 25.69, 'Mg': 34.87, 'Al': 78.23, 'Si': 107.7, 'P': 75.42, 'S': 65.66, 'Cl': 28.5901,
'K': 36.841, 'Ca': 41.014, 'Ti': 111.2, 'Cu': 79.16, 'Zn': 29.685, 'Ge': 87.1, 'Br': 28.1821,
'Kr': -1.481,
'Rb': 17.86, 'Ag': 66.61, 'Cd': 25.240, 'Sn': 70.50, 'I': 24.04, 'Xe': -1.481,
'Rb': 17.86, 'Ag': 66.61, 'Cd': 25.240, 'Sn': 70.50, 'I': 25.6111, 'Xe': -1.481,
'Cs': 16.80, 'Hg': 13.19, 'Pb': 15.17}

# Thermal contribution to enthalpy for the atoms reported by Gaussian thermo whitepaper
# This will be subtracted from the corresponding value in atom_hf to produce an enthalpy used in calculating
# the enthalpy of formation at 298 K
atom_thermal = {'H': 1.01, 'He': 1.481,
'Li': 1.1, 'Be': 0.46, 'B': 0.29, 'C': 0.25, 'N': 1.04, 'O': 1.04, 'F': 1.05, 'Ne': 1.481,
'Na': 1.54, 'Mg': 1.19, 'Al': 1.08, 'Si': 0.76, 'P': 1.28, 'S': 1.05, 'Cl': 1.1,
'K': 1.481, 'Ca': 1.481, 'Ti': 1.802, 'Cu': 1.481, 'Zn': 1.481, 'Ge': 1.768, 'Br': 1.481,
atom_thermal = {'H': 1.012, 'He': 1.481,
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@dranasinghe dranasinghe May 20, 2020

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There is a problem with how H( 0 k) and H(298K) presented, each uses their own standard state. So it Looks like I have to email ATCT and request thermal correction relative to H(298 K)

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@cgrambow cgrambow May 20, 2020

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Aren't atom_thermal just ideal gas corrections? They shouldn't change, right?

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@dranasinghe dranasinghe May 20, 2020

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I think they depend on Cp (int Cp=0 to Cp 298)

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@dranasinghe dranasinghe May 20, 2020

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Let's make sure.

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@cgrambow cgrambow May 20, 2020

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Yes, they're the enthalpy increment of the elements (or 1/2 for diatomic reference states). Translational and rotational contributions are constant. If the vibrational frequencies of diatomics have changed in recent times, then the vibrational contribution could have changed, and if the excited state energy levels have changed in recent times, then the electronic contribution could have changed. My assumption would be that the frequencies and energy levels of diatomics are very well known, so these numbers should be accurate. I'll try to find recent frequencies and energy levels to calculate some of these numbers and see if my calculations agree.

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@dranasinghe dranasinghe May 20, 2020 •
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We do 2 for loops in [RMG-Py/arkane/encorr/corr.py](https://github.com/ReactionMechanismGenerator/RMG-Py/blob/74cee80a8c688b04dba265b2bb0b2a10724bee41/arkane/encorr/corr.py#L140) line 120 to 140. I Don't see a problem replacing with one for loop and use the J as units.

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@cgrambow cgrambow May 20, 2020

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Yes, it'll be exactly the same combining them into one number. What I'm trying to say is that it's better having them separate in the database because it makes for easier comparison with literature. For example, ATcT only lists atom_hf so a direct comparison to ATcT wouldn't be easy if we combine the numbers in the database.

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@dranasinghe dranasinghe May 20, 2020

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I agree with your comment that it would be easy to compare but the way we use/code we would never able to use that data. So why not combine?

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@cgrambow cgrambow May 20, 2020

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The way that Arkane separates all the terms (and then adds them back together) is the standard way to compute thermochemistry in literature, so I think we should keep it the way it is.

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@cgrambow cgrambow May 20, 2020

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By the way, I calculated the thermal corrections for all the gas phase diatomics, and my calculations agree with the values in the database.

'Li': 1.1, 'Be': 0.46, 'B': 0.29, 'C': 0.2512, 'N': 1.036, 'O': 1.037, 'F': 1.055, 'Ne': 1.481,
'Na': 1.54, 'Mg': 1.19, 'Al': 1.08, 'Si': 0.76, 'P': 1.28, 'S': 1.054, 'Cl': 1.097,
'K': 1.481, 'Ca': 1.481, 'Ti': 1.802, 'Cu': 1.481, 'Zn': 1.481, 'Ge': 1.768, 'Br': 2.930,
'Kr': 1.481,
'Rb': 1.481, 'Ag': 1.481, 'Cd': 1.481, 'Sn': 1.485, 'I': 1.481, 'Xe': 1.481,
'Rb': 1.481, 'Ag': 1.481, 'Cd': 1.481, 'Sn': 1.485, 'I': 1.577, 'Xe': 1.481,
'Cs': 1.481, 'Hg': 1.481, 'Pb': 1.481}

# Spin orbit correction (SOC) in Hartrees
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