Arkane: add check for iop(2/9=2000) in Gaussian load geometry#2758
Arkane: add check for iop(2/9=2000) in Gaussian load geometry#2758rwest merged 3 commits intoReactionMechanismGenerator:mainfrom
Conversation
|
This is currently failing the unit tests because the toluene and benzyl Arkane examples have Gaussian logfiles with more than 14 atoms. I'm rerunning these calculations to see how much it changes the results. If it's a lot, I'll replace the logfiles. If it's not much, that means I've been overstating the error due to this bug and I may not fully understand the problem I thought I was diagnosing. |
|
This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days. |
github-actions
bot
added
the
abandoned
|
@sevyharris I see that this PR fell off - want to revive? |
sevyharris
removed
stale
|
This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days. |
|
This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days. |
github-actions
bot
added
the
abandoned
rwest
removed
stale
There is concern that Gaussian was not run with iop(2/9=2000) which means that when there are 14 or more atoms, the Hessian is output in a different coordinate system from the geometry, which can lead to incorrect frequencies when projecting out the hindered rotors, which can lead to erroneous entropy values and hence bad Gibbs energies. See ReactionMechanismGenerator/RMG-Py#2758 and ReactionMechanismGenerator/RMG-Py#2757
|
It fails the unit test, because a log file for Toluene.
Is the test too restrictive? or should the log file be replaced? or...? |
So, as we just saw with David's workflow, I think the problem is only when you combine optimization and frequency. Here, frequency is its own separate calculation, so it's fine. I should add a check to see if the Gaussian job did any optimization in the same job as the frequency calculations. |
This overlay keeps the Hessian in input orientation, but it's only required when you do an optimization. If it's just a frequency calculation, it is unnecessary.
sevyharris
force-pushed
the
iop29_warning
branch
from
2099a34 to
ad04e92
Compare
|
I changed it so it only raises this error if it's grabbing a Hessian from a calculation that also included an optimization (which might change the orientation). So calculations like the Arkane examples that just do the frequency are fine. It should now pass the test it was failing earlier. |
Regression Testing Results
Detailed regression test results.Regression test aromatics:Reference: Execution time (DD:HH:MM:SS): 00:00:00:55 aromatics Passed Core Comparison ✅Original model has 15 species. aromatics Failed Edge Comparison ❌Original model has 106 species. Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-CsCsHH) + group(Cds-CdsCsCs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + Estimated bicyclic component: polycyclic(s2_3_5_ane) - ring(Cyclopropane) - ring(Cyclopentane) + ring(Cyclopentene) + ring(Cyclopropane) + polycyclic(s2_3_6_ene_1) + polycyclic(s3_5_6_diene_1_5) - ring(Cyclopropane) - ring(Cyclopentene) - ring(Cyclohexene) + radical(cyclopentene-4) Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsCs) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-CsCsHH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + polycyclic(s2_4_4_ene_1) + polycyclic(s1_4_5_diene_1_6) + polycyclic(s3_4_5_ene_1) - ring(Cyclobutene) - ring(Cyclobutane) - ring(Cyclopentene) + radical(bicyclo[2.1.1]hex-2-ene-C5) Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(Cs-CsCsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsCsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds- Cds(Cds-Cds)Cs) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + polycyclic(s2_3_5_ene_1) + polycyclic(s2_3_6_ene_1) + Estimated bicyclic component: polycyclic(s3_5_6_ane) - ring(Cyclopentane) - ring(Cyclohexane) + ring(Cyclopentene) + ring(Cyclohexene) - ring(Cyclopropane) - ring(Cyclopentene) - ring(Cyclohexene) + radical(cyclopentene-allyl) Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsCsH) + group(Cdd-CdsCds) + Estimated bicyclic component: polycyclic(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(124cyclohexatriene) + ring(1,4-Cyclohexadiene) Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)CsHH) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + Estimated bicyclic component: polycyclic(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(1,3-Cyclohexadiene) + ring(1,3-Cyclohexadiene) Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds- CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsHH) + Estimated bicyclic component: polycyclic(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(1,3-Cyclohexadiene) + ring(1,3-Cyclohexadiene) + radical(Cds_P) Non-identical thermo! ❌
thermo: Thermo group additivity estimation: group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cs-(Cds-Cds)(Cds-Cds)CsH) + group(Cds-Cds(Cds-Cds)(Cds-Cds)) + group(Cds- CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-CdsCsH) + group(Cds-Cds(Cds-Cds)H) + group(Cds-Cds(Cds-Cds)H) + group(Cds-CdsHH) + Estimated bicyclic component: polycyclic(s4_6_6_ane) - ring(Cyclohexane) - ring(Cyclohexane) + ring(1,3-Cyclohexadiene) + ring(1,3-Cyclohexadiene) Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics: DetailsObservables Test Case: Aromatics Comparison✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions! aromatics Passed Observable Testing ✅Regression test liquid_oxidation:Reference: Execution time (DD:HH:MM:SS): 00:00:01:57 liquid_oxidation Passed Core Comparison ✅Original model has 37 species. liquid_oxidation Failed Edge Comparison ❌Original model has 214 species. Non-identical kinetics! ❌
kinetics: DetailsObservables Test Case: liquid_oxidation Comparison✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! liquid_oxidation Passed Observable Testing ✅Regression test nitrogen:Reference: Execution time (DD:HH:MM:SS): 00:00:01:03 nitrogen Passed Core Comparison ✅Original model has 41 species. nitrogen Passed Edge Comparison ✅Original model has 133 species. DetailsObservables Test Case: NC Comparison✅ All Observables varied by less than 0.200 on average between old model and new model in all conditions! nitrogen Passed Observable Testing ✅Regression test oxidation:Reference: Execution time (DD:HH:MM:SS): 00:00:01:44 oxidation Passed Core Comparison ✅Original model has 59 species. oxidation Passed Edge Comparison ✅Original model has 230 species. DetailsObservables Test Case: Oxidation Comparison✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions! oxidation Passed Observable Testing ✅Errors occurred during observable testing
WARNING:root:Initial mole fractions do not sum to one; normalizing.
|
3 participants
Motivation or Problem
By default, Gaussian only prints Cartesians in the input orientation for small cases. Add a check for the IOP(2/9=2000) keyword so users don't get tripped up like I did here: #2757 with coordinates that don't match the Hessian.
Description of Changes
I added a check for the IOP(2/9=2000 keyword) when loading the geometry. If the molecule has 14+ atoms (this seems to be the threshold according to my experiments), this will raise a LogError if the keyword hasn't been specified.
Testing
I tested this using one Gaussian logfile that has the IOP and one that doesn't.
conformer_0002_iop.log
conformer_0002_no_iop.log