Change method for loading energies from Gaussian log files to regex search to avoid errors #2595
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I know this isn't ready yet, but when you are good for review please squash these commits. Thanks! |
donerancl
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I think this is ready. I was able to parse thousands of gaussian log files without the errors from the issue I described above. |
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Thanks for squashing! The new regex seems to work, as it isn't failing any such tests.
This is failing a couple of the other unit tests - it seems that the new Energy= test is picking up some non-numeric text in some cases, like in this unit test: https://github.com/ReactionMechanismGenerator/RMG-Py/actions/runs/7732973138/job/21084096743?pr=2595#step:10:2616
which is attempting to read this Gaussian log file: https://github.com/ReactionMechanismGenerator/RMG-Py/blob/b53f63bf7826440c1e410e311136fa606167c332/arkane/data/gaussian/oxygen.log
It picks up either "change" or "forces"
Regression Testing Results
Detailed regression test results.Regression test aromatics:Reference: Execution time (DD:HH:MM:SS): 00:00:01:05 aromatics Passed Core Comparison ✅Original model has 15 species. aromatics Passed Edge Comparison ✅Original model has 106 species.
Observables 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): 00:00:02:09 liquid_oxidation Failed Core Comparison ❌Original model has 37 species. Non-identical kinetics! ❌
kinetics: liquid_oxidation Failed Edge Comparison ❌Original model has 202 species. Non-identical kinetics! ❌
kinetics:
Observables 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): 00:00:01:22 nitrogen Passed Core Comparison ✅Original model has 41 species. nitrogen Passed Edge Comparison ✅Original model has 132 species.
Observables 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): 00:00:02:25 oxidation Passed Core Comparison ✅Original model has 59 species. oxidation Passed Edge Comparison ✅Original model has 230 species.
Observables 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 ✅Regression test sulfur:Reference: Execution time (DD:HH:MM:SS): 00:00:00:54 sulfur Passed Core Comparison ✅Original model has 27 species. sulfur Failed Edge Comparison ❌Original model has 89 species.
Observables Test Case: SO2 Comparison
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! sulfur Passed Observable Testing ✅Regression test superminimal:Reference: Execution time (DD:HH:MM:SS): 00:00:00:34 superminimal Passed Core Comparison ✅Original model has 13 species. superminimal Passed Edge Comparison ✅Original model has 18 species. Regression test RMS_constantVIdealGasReactor_superminimal:Reference: Execution time (DD:HH:MM:SS): 00:00:02:29 RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅Original model has 13 species. RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅Original model has 13 species.
Observables Test Case: RMS_constantVIdealGasReactor_superminimal Comparison
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅Regression test RMS_CSTR_liquid_oxidation:Reference: Execution time (DD:HH:MM:SS): 00:00:06:11 RMS_CSTR_liquid_oxidation Passed Core Comparison ✅Original model has 37 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 206 species. Non-identical kinetics! ❌
kinetics:
Observables Test Case: RMS_CSTR_liquid_oxidation Comparison
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! RMS_CSTR_liquid_oxidation Passed Observable Testing ✅Regression test fragment:Reference: Execution time (DD:HH:MM:SS): 00:00:00:40 fragment Passed Core Comparison ✅Original model has 10 species. fragment Passed Edge Comparison ✅Original model has 33 species.
Observables Test Case: fragment Comparison
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! fragment Passed Observable Testing ✅Regression test RMS_constantVIdealGasReactor_fragment:Reference: Execution time (DD:HH:MM:SS): 00:00:03:08 RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅Original model has 10 species. RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅Original model has 27 species.
Observables Test Case: RMS_constantVIdealGasReactor_fragment Comparison
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! RMS_constantVIdealGasReactor_fragment Passed Observable Testing ✅beep boop this comment was written by a bot 🤖 |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #2595 +/- ##
==========================================
+ Coverage 54.79% 55.15% +0.35%
==========================================
Files 125 125
Lines 37156 37037 -119
==========================================
+ Hits 20361 20427 +66
+ Misses 16795 16610 -185 ☔ View full report in Codecov by Sentry. |
JacksonBurns
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Rebased and enabled auto-merge, so this should go in on its own tonight. |
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Arg this is blocked by CI issues, apologies. Addressing now, will circle back to this... |
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Issue found, blocked by #2608 |
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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. |
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Now blocked by #2658 |
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Regression Testing ResultsWARNING:root:Initial mole fractions do not sum to one; normalizing. Detailed regression test results.Regression test aromatics:Reference: Execution time (DD:HH:MM:SS): 00:00:01:06 aromatics Passed Core Comparison ✅Original model has 15 species. aromatics Passed Edge Comparison ✅Original model has 106 species.
Observables 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): 00:00:02:10 liquid_oxidation Failed Core Comparison ❌Original model has 37 species. Non-identical kinetics! ❌
kinetics: liquid_oxidation Failed Edge Comparison ❌Original model has 202 species. Non-identical kinetics! ❌
kinetics: Non-identical kinetics! ❌
kinetics:
Observables 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): 00:00:01:23 nitrogen Failed Core Comparison ❌Original model has 41 species. nitrogen Failed Edge Comparison ❌Original model has 132 species.
Observables 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): 00:00:02:23 oxidation Passed Core Comparison ✅Original model has 59 species. oxidation Passed Edge Comparison ✅Original model has 230 species.
Observables 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 ✅Regression test sulfur:Reference: Execution time (DD:HH:MM:SS): 00:00:00:55 sulfur Passed Core Comparison ✅Original model has 27 species. sulfur Failed Edge Comparison ❌Original model has 89 species.
Observables Test Case: SO2 Comparison
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! sulfur Passed Observable Testing ✅Regression test superminimal:Reference: Execution time (DD:HH:MM:SS): 00:00:00:35 superminimal Passed Core Comparison ✅Original model has 13 species. superminimal Passed Edge Comparison ✅Original model has 18 species. Regression test RMS_constantVIdealGasReactor_superminimal:Reference: Execution time (DD:HH:MM:SS): 00:00:02:22 RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅Original model has 13 species. RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅Original model has 13 species.
Observables Test Case: RMS_constantVIdealGasReactor_superminimal Comparison
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅Regression test RMS_CSTR_liquid_oxidation:Reference: Execution time (DD:HH:MM:SS): 00:00:05:56 RMS_CSTR_liquid_oxidation Passed Core Comparison ✅Original model has 37 species. RMS_CSTR_liquid_oxidation Passed Edge Comparison ✅Original model has 206 species.
Observables Test Case: RMS_CSTR_liquid_oxidation Comparison
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! RMS_CSTR_liquid_oxidation Passed Observable Testing ✅Regression test fragment:Reference: Execution time (DD:HH:MM:SS): 00:00:00:40 fragment Passed Core Comparison ✅Original model has 10 species. fragment Passed Edge Comparison ✅Original model has 33 species.
Observables Test Case: fragment Comparison
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! fragment Passed Observable Testing ✅Regression test RMS_constantVIdealGasReactor_fragment:Reference: Execution time (DD:HH:MM:SS): 00:00:03:02 RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅Original model has 10 species. RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅Original model has 27 species.
Observables Test Case: RMS_constantVIdealGasReactor_fragment Comparison
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! RMS_constantVIdealGasReactor_fragment Passed Observable Testing ✅Regression test minimal_surface:Reference: Execution time (DD:HH:MM:SS): 00:00:01:06 minimal_surface Passed Core Comparison ✅Original model has 30 species. minimal_surface Passed Edge Comparison ✅Original model has 131 species.
Observables Test Case: minimal_surface Comparison
✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions! minimal_surface Passed Observable Testing ✅beep boop this comment was written by a bot 🤖 |
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No longer blocked, going to enable auto-merge, rebase, and let this go in. Thanks @donerancl! |
JacksonBurns
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@hwpang please review as well |
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Rebasing with #2669 now merged (hopefully) fixing CI |
I think I added these in accidentally, I got the same error and omitting them fixed it
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en-pretty-fy whitespace Co-authored-by: Hao-Wei Pang <[email protected]>
that's what i get for copy-pasting from the README
JacksonBurns
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Regression Testing ResultsWARNING:root:Initial mole fractions do not sum to one; normalizing. Detailed regression test results.Regression test aromatics:Reference: Execution time (DD:HH:MM:SS): 00:00:01:06 aromatics Passed Core Comparison ✅Original model has 15 species. aromatics Passed Edge Comparison ✅Original model has 106 species.
Observables 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): 00:00:02:08 liquid_oxidation Passed Core Comparison ✅Original model has 37 species. liquid_oxidation Passed Edge Comparison ✅Original model has 202 species.
Observables 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): 00:00:01:22 nitrogen Passed Core Comparison ✅Original model has 41 species. nitrogen Passed Edge Comparison ✅Original model has 132 species.
Observables 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): 00:00:02:22 oxidation Passed Core Comparison ✅Original model has 59 species. oxidation Passed Edge Comparison ✅Original model has 230 species.
Observables 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 ✅Regression test sulfur:Reference: Execution time (DD:HH:MM:SS): 00:00:00:54 sulfur Passed Core Comparison ✅Original model has 27 species. sulfur Failed Edge Comparison ❌Original model has 89 species.
Observables Test Case: SO2 Comparison
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! sulfur Passed Observable Testing ✅Regression test superminimal:Reference: Execution time (DD:HH:MM:SS): 00:00:00:34 superminimal Passed Core Comparison ✅Original model has 13 species. superminimal Passed Edge Comparison ✅Original model has 18 species. Regression test RMS_constantVIdealGasReactor_superminimal:Reference: Execution time (DD:HH:MM:SS): 00:00:02:20 RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅Original model has 13 species. RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅Original model has 13 species.
Observables Test Case: RMS_constantVIdealGasReactor_superminimal Comparison
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅Regression test RMS_CSTR_liquid_oxidation:Reference: Execution time (DD:HH:MM:SS): 00:00:05:51 RMS_CSTR_liquid_oxidation Passed Core Comparison ✅Original model has 37 species. RMS_CSTR_liquid_oxidation Passed Edge Comparison ✅Original model has 206 species.
Observables Test Case: RMS_CSTR_liquid_oxidation Comparison
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! RMS_CSTR_liquid_oxidation Passed Observable Testing ✅Regression test fragment:Reference: Execution time (DD:HH:MM:SS): 00:00:00:41 fragment Passed Core Comparison ✅Original model has 10 species. fragment Passed Edge Comparison ✅Original model has 33 species.
Observables Test Case: fragment Comparison
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! fragment Passed Observable Testing ✅Regression test RMS_constantVIdealGasReactor_fragment:Reference: Execution time (DD:HH:MM:SS): 00:00:03:04 RMS_constantVIdealGasReactor_fragment Passed Core Comparison ✅Original model has 10 species. RMS_constantVIdealGasReactor_fragment Passed Edge Comparison ✅Original model has 27 species.
Observables Test Case: RMS_constantVIdealGasReactor_fragment Comparison
✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions! RMS_constantVIdealGasReactor_fragment Passed Observable Testing ✅beep boop this comment was written by a bot 🤖 |
Motivation or Problem
Sometimes, in gaussian log files, the line that contains the energy has extra characters (more than one line printed in the same line) that prevent the load_energy function in arkane/ess/gaussian.py from parsing the energy. (e.g., it will try to use an "=" as the energy)
Description of Changes
Before: find the line that has "SCF Done:", split it, take the 4th index as the energy
After: find the line that has "SCF Done:", find the substring that matches "SCF Done: E(...) = {energyfloat}, split the substring, and take the last item
the same can be done for E2, MP2, E(CORR), CCSD(T), CBS-QB3 (0 K), E(CBS-QB3)=, CBS-4 (0 K)=, G3(0 K), G3 Energy=,G4(0 K), G4 Energy=, G4MP2(0 K), G4MP2 Energy= in the same function
Testing
I plan to try the load_energy function on many gaussian log files, some which have extra characters in the line containing the energy
Reviewer Tips
Suggestions for verifying that this PR works or other notes for the reviewer.