RMG-database version 3.3.0
#697
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- remove gitter, which we do not monitor - add link to rmg-py which has the docs for everything
one was in python 2, has clearly not been run in some time
small changes to the checkout commands, docs updates throughout
Rebuild CI to use RMG-Py
- only run on linux; nothing we do here can break macos - copy the environment building steps from RMG-Py ci to fix the directory issue that is preventing regression testing from working here - pull stable results from rmg-py instead of regenerating them here asdf
Fix Regression Testing Issue by Simplifying CI to Match RMG-Py, and fixing the path.
Update and add BEP rules for surface families. Thanks @bjkreitz !
… format fix Surface_Abstraction training reactions format
It's the reverse of Surface_Abstraction_Beta_vdW, which is better named and has some data.
The family has been removed. Delete it's png
Fix failing CI due to Python 3.9 changes
Add Fe110 to metal database
Values taken from:
Xu L, Kirvassilis D, Bai Y, Mavrikakis M. Atomic and molecular adsorption on Fe(110).
Surface science. 2018;667:54-65. doi:10.1016/j.susc.2017.09.002
The lattice constant PW91 is given in the paper as a=2.85 Angstrom.
Then surface site density was calculated using the following code
import ase.build
import numpy as np
import ase.visualize
import rmgpy.constants
a = 2.85 # A
surface = ase.build.bcc110("Fe", (3, 3, 3), a=a, periodic=True)
a1 = surface.cell[0]
a2 = surface.cell[1]
unit_cell_area = np.linalg.norm(np.cross(a1, a2))
print(f'Unit cell area:\t{area:0.5f}\tA^2')
site_area = unit_cell_area / 9.0
print(f'Site area:\t{site_area:0.5f}\t\tA^2/site')
print(f'Site density:\t{1.0 / site_area:0.5f}\t\tsites/A^2')
SDEN = 1.0 / site_area * (1e20) / rmgpy.constants.Na
print(f'Site density:\t{SDEN:0.5e}\tmols/m^2')
SDEN = 1.0 / site_area * (1e16) / rmgpy.constants.Na
print(f'Site density:\t{SDEN:0.5e}\tmols/cm^2')
Small `conda` recipe fixes for RMG-Py `conda` fix
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): 00:00:00:50 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)(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 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:
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): 00:00:01:56 liquid_oxidation Passed Core Comparison ✅Original model has 37 species. liquid_oxidation Failed Edge Comparison ❌Original model has 214 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): 00:00:00:58 nitrogen Passed Core Comparison ✅Original model has 41 species. nitrogen Passed Edge Comparison ✅Original model has 133 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): 00:00:01:32 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): 00:00:00:38 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): 00:00:00:25 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): 00:00:02:17 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): 00:00:10:44 RMS_CSTR_liquid_oxidation Failed Core Comparison ❌Original model has 35 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 99 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 ✅beep boop this comment was written by a bot 🤖 |
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Thanks Jackson. I think all the changes have been reviewed as they were merged into main, so I'm not going to go over those again. |
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@rwest thanks! The upload step is here: https://github.com/ReactionMechanismGenerator/RMG-database/blob/main/.github/workflows/conda_build.yml#L41-L44 On completion of the build and subsequent test, the builds will automatically be uploaded, only on pushes to |
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waaait - wouldn't we want #694 to be in the release? |
rwest
dismissed
their stale review
Pausing to consider if we want #694 included. Otherwise we have an official release with knowingly broken notebooks?
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#694 is almost done; it's just missing (potential) updates to the |
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If we release the |
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How about we merge in the existing changes then, and post an Issue to revisit the AEC/BAC notebooks? If we want to do this PR #694 is ready to go from my end. |
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That sounds good to me. |
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Those changes will automatically be reflected here when the PR is merged. I will update the description, and then merge this PR once ready. |
Update Jupyter notebooks and associated codebase [RMG-database]
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): 00:00:00:52 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)(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(124cyclohexatriene) 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:
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): 00:00:02:02 liquid_oxidation Passed Core Comparison ✅Original model has 37 species. liquid_oxidation Failed Edge Comparison ❌Original model has 214 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): 00:00:00:58 nitrogen Passed Core Comparison ✅Original model has 41 species. nitrogen Passed Edge Comparison ✅Original model has 133 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): 00:00:01:31 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): 00:00:00:38 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): 00:00:00:25 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): 00:00:03:00 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): 00:00:14:07 RMS_CSTR_liquid_oxidation Failed Core Comparison ❌Original model has 35 species. RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌Original model has 107 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 ✅beep boop this comment was written by a bot 🤖 |
This PR from
mainintostablewill trigger the release ofrmgdatabase =3.3.0. This contains ~2 years of work by many contributors.When this is merged,
condabinaries will automatically be built and uploaded to thermgconda channel.Below is a draft release for the official GitHub Release (members of the development team can view this here), please let me know your thoughts:
RMG-database Version 3.3.0
This release marks the first official RMG-database release in two years! There are many bug fixes, new features, new data entries, and software improvements - see the full list below.
This release will be done alongside RMG-Py v3.3.0 which also includes a number of new features, bug fixes, and exciting improvements.
What's new?
Continuous integration overhauls and upgrades:
condarecipe fixed:condarecipe fixes for RMG-Pycondafix by @JacksonBurns in Smallcondarecipe fixes for RMG-Pycondafix #696Various small bug fixes:
New features:
New and updated data:
Full Changelog: 3.2.0...3.3.0
New Contributors