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Difficulty with [H] (and perhaps other atomic species) #435

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mjohnson541 opened this issue Oct 30, 2020 · 7 comments · May be fixed by #436
Open

Difficulty with [H] (and perhaps other atomic species) #435

mjohnson541 opened this issue Oct 30, 2020 · 7 comments · May be fixed by #436
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Type: Bug

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@mjohnson541
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When I run [H] at CBS-QB3 I get:

Species [H] failed with status:
{'conformers': False, 'fine': False, 'freq': False, 'irc': True, 'opt': False, 'rotors': True, 'sp': False}
and errors: Error: Could not troubleshoot composite for [H]! Tried troubleshooting with the following methods: ['int=(Acc2E=14)']; Error: Could not troubleshoot composite for [H]! Tried troubleshooting with the following methods: ['int=(Acc2E=14)']; Error: Could not troubleshoot composite for [H]! Tried troubleshooting with the following methods: ['restart_due_to_file_not_found', 'int=(Acc2E=14)']; Error: Could not troubleshoot composite for [H]! Tried troubleshooting with the following methods: ['int=(Acc2E=14)']; Error: Could not troubleshoot composite for [H]! Tried troubleshooting with the following methods: ['int=(Acc2E=14)']; Error: Could not troubleshoot composite for [H]! Tried troubleshooting with the following methods: ['int=(Acc2E=14)']; Error: Could not troubleshoot composite for [H]! Tried troubleshooting with the following methods: ['int=(Acc2E=14)'];

Of course we don't usually need to specifically calculate [H], but this seems to prevents ARC from automatically calculating the rate coefficient of reactions [H] participates in even if it doesn't need [H] for the forward rate coefficient.
@xiaoruiDong
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I haven't had a chance to use ARC to calculate an atomic species. Matt, can you upload an example of your [H] QM calculation output? (something like output.out / input.log) Also, can you upload arc.log, if it is not super large? I feel like the isomorphism check can be problematic but just need to check calculations are all good and if there is any helpful error message in the output file. Thanks.

@mjohnson541
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Yep, thanks for taking a look!

input.txt
output.txt
arc.log

@alongd alongd linked a pull request Nov 1, 2020 that will close this issue
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@dranasinghe
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Looks like this is a problem with G09 , I think Gaussin fix it in G16. I was able to successfully run a job in G09 when I used
#P cbs-qb3 iop(1/18=1)
IOp(1./18=1) will stop any geometry optimization.

@alongd
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alongd commented Nov 1, 2020

Thanks for the input. So it seems important for g09 and harmless for g16 to add iop(1/18=1) to all composite methods involving a monoatomic species. Let's do that

@dranasinghe
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dranasinghe commented Nov 1, 2020 via email

@alongd
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alongd commented Nov 7, 2020

OK, added.
@mjohnson541, can you try again?

@alongd
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alongd commented Jun 27, 2021 •
edited

I bumped into this issue in ARC, it was also solved by removing guess=mix or guess=read for monoatomic species. I'll make a PR.
Edit: a fix will be added to the future Job PR (where the Gaussian job module was re-written)

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Use "calcfc" in Gaussian only for non monoatomic species ReactionMechanismGenerator/ARC
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@mjohnson541 @alongd @dranasinghe @xiaoruiDong