Nate Harms

Parameter parsing fails for strings containing `=` character

2

Hello there! I'm using Papermill to automate some Jupyter notebook execution and I think I may have caught a potential bug: when running Papermill using strings containing a `=` character...

I just saw that ASE now has native TS optimizers and IRC calculations for Gaussian. This may be worth looking into 🤔 See the link below: https://wiki.fysik.dtu.dk/ase/dev/ase/calculators/gaussian.html

Building of TSs with reactant and product species geometries

1

Conformational changes like inversion of chiral centers and rotation about double bonds rarely occur when reactants go to TSs (e.g. a reactant containing a cis double bond will probably have...

Currently the testing around validating IRCs is a bit lax (as seen in PR #52). We should make a test that reads an existing IRC calculation and validated (and /...

Symmetry number estimations not always accurate

4

Symmetry numbers calculated using RMG's `symmetry` package tend to result in incorrect estimations of symmetry numbers. Below is an example of ethane which should have a symmetry number of [6](https://webbook.nist.gov/cgi/cbook.cgi?ID=C74840&Mask=800)....

Unit tests currently exist but are very sparse right now for the update methods. This was caught in PR #43 but will be addressed within this issue

From reading about other tools, many will `template` when generating a TS guess. From the AutoTS paper > In addition to interpolation, we have the ability to use geometric information...

Due to lack of Gaussian on all computing clusters, we are hoping to add additional calculators to AutoTST: - [ ] NWChem - [ ] MolPro Any additional suggestions?

Currently, AutoTST can generate calculators and write input files for 1-D hindered rotor scans, however, there is a lot of fine tuning that needs to be done in order for...

Once #13 #16 and #14 are closed, the example scripts should be updated to work with / demonstrate AutoTST effectively.