Merge stable into main before v3.2.0 #621
Closed
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
I assume some isomorphism checker neglected the multiplicity and thought CH2 and CH2(S) were isomorphic, and CH2CHN(S) and CH2CHN, so it merged the kinetics and/or marked things as duplicates when they shouldn't be. This commit fixes that, but unfortunately the numbering is now off and there are multiple reactions with the same index attribute.
Add Abraham solvent parameters and dielectric constant for (1) methanol, (2) methanol-water mixture (v50:50), (3) acetonitrile-water mixture (v40:60 and v60:40)
For each solvent, 'name_in_coolprop' is added as a new feature of solventData. CoolProp is an external packaged used for fluid properties calculations. It takes a solvent's name as an input which is saved as 'name_in_coolprop'. If solvents are not availalbe in CoolProp, its 'name_in_coolprop' is set to None.
by a rad adjacent to the ring at the far end sites (symmetric, so only one forbidden group was added)
Previously, using `str(reaction)`, called the `__str__` method for `RMG-Py/rmgpy/reaction.py` which used the index when creating the kinetics library: `reactions.py`. However, this format was inconsistent with the corresponding `dictionary.txt` that did NOT use indices. The fix is to instead call the `to_labeled_str` method, whose default sets the `use_index` flag to `False`, thus making the format consistent.
Remove whitespace around keyword arguments
Its reference enthalpy of formation obtained from CCCBDB is incorrect. A more correct value is available in ATcT but is not included here because its uncertainty is too large.
The wb97m-v/def2-tzvpd calculation for dinitrogen dioxide had the incorrect geometry. Update geometry and add updated enthalpy of formation.
The mercaptomethyl reference enthalpy was parsed incorrectly from the literature. It actually corresponds to the methylthio radical. The mercaptomethyl value is not updated because its literature value has very large uncertainty. Methylthio is not added to the reference database because it is difficult to converge in C3v symmetry, most likely due to a Jahn-Teller effect similar to the methoxy radical.
Previously this data was stored in RMG-Py, but data like this should be stored in RMG-database
Likely due to an incorrect assignment of a smiles string that propagated to the other changes. It appears that the QM data is valid though, as the QM data has the correct number of atoms in each case
the barrier is way too low to be correct and we have much much better data in the reverse
Now use Surface_Dissociation instead
remove Surface_Recombination family
Making this family for single-bonded species reacting with van der waals species as a surface abstraction reaction. Create rules.py A copy of Surface_Abstraction_vdW family
Think this might need some hard-coding in RMG-Py to switch the labels. Note: you must put group names in right order. If your tree is in a different order from your rules then the database tests fail.
I don't have ImageMagick so rather than convert the eps I just saved as a png from ChemDraw, but it looks about the same as the others.
A merge of several commits: update the format of the template rename family's name as Surface_Adsorption_Dissociation_Double and add O2 reaction to rules.py fix recipe, parent-child relationships and Entry errors
I had an issue with the eps converting process, so the png file was saved from ChemDraw
entry 11 should be
multiplicity [1]
1 *2 N u0 p1 c0 {2,D}
2 *3 C u0 p0 c0 {1,D}
rather than
multiplicity [1]
1 *2 N u0 p1 c0 {2,D}
2 *3 C u0 p1 c0 {1,D}
Making it match the RMG-Py workflow more closely. Using setup-miniconda action. Splitting job into parts. Better management of dual PRs that need a different RMG-Py branch. Rename the deploy.sh to trigger-rmg-tests.sh
This just leaves the deploy, and I'm not sure if it works.
This travis file is now only used for deployment of conda builds, and I'm not sure if it works. But might as well update this anyway.
|
Created this just to compare main and stable branches since it says that stable is 139 commits ahead of main. It's not actually |
|
creating a new PR using a different branch that does the same? |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
16 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.