Kinbot

Major improvements and changes:
* Support for new codes
* QChem can be used as quantum chemistry code.
* Orca can now be used as L3 (CCSD(T)) code.
* Upgrade to be compatible with official ASE v3.10.
* Upgrade to be compatible with Molpro 2022.
* Improved UQ:
* Added hindered rotor UQ formulation.
* Improved tunneling uncertainty implementation.
* Includes UQ in phase-space theory and collisional energy transfer parameters.
* Implemented Multi-conformer TST.
* PES postprocess and analysis:
* Perform T1 diagnostics statistics at the end of a PES execution.
* Perform L2-L3 energy difference analysis statistics.
* Improved installation:
* Use official ASE version instead of custom one.
* Make conda and pip packages.
* PES postprocess and analysis:
* Added interactive PES graph visualization through [PESViewer.](https://github.com/rubenvdvijver/PESViewer)

Minor improvements:
* Homolytic scissions are now treated as reaction families (hom_sci family).
* Improved robustness of templates and reaction recipes.
* Allow to run locally by just checking files.
* Avoid performing Optimize on skipped chemids.
* Allow small negative frequencies (> -50 cm-1) for wells.
* Added chirality check.
* Retry some failed calculations with cartesian coordinates.
* Improved documentation and message printing/logging.

Bug fixes.

Major improvements and changes:
* Added in the ability to have Cl, Br, I and F as part of your molecule.
* Note: No reactions involving these molecules have been added yet.
* KinBot now checks rotor types to see if they are hindered or free.
* Template files for including free rotors in MESS input files have been added.
* New JSON file parameters have been added to KinBot
* free_rotor_thrs – energy threshold for free rotors
* epsilon_units – units used in MESS file for epsilon parameter, can be K, J/mol or cm-1
* New reaction class for homolytic scissions has been added to reaction_generator
* Homolytic scissions are now considered a reaction family and are searched for during KinBot’s reaction generation step.
* The hom_sci keyword can be specified if the families or skip_families keywords are being used.
* There is no longer a need to turn on the homolytic_scissions parameter within the JSON input file.
* MESS files have been updated to include the following parameters
* MicroRateOutput
* MicroEnerMax[kcal/mol]
* MicroEnerMin[kcal/mol]
* MicroEnerStep[kcal/mol]
* Bug fixes

Major improvements and changes:
* New/improved families for Korcek reactions and internal OH migration
* New family to search for barrierless reactions at a level different from the other searches (L1, L2, L3)
* Possibility to request AM1 conformational scans to speed up search for large molecules
* Arbitrary conformer search grid can be requested
* Reaction families are moved into a separate directory in the code
* Mess printing is greatly improved, both at the level of the code and at the outcome (nicer look etc.). SMILES of species is printed in MESS in comment
* ZPE is now included in the reaction barrier threshold - can lead to different outcomes as previous versions for reactions around the threshold!
* Possible to request rigid hindered rotor scans
* Hindered rotor barriers are cut above 20 kcal/mol to avoid oscillations in Fourier fit in MESS
* UQ code is working on the KinBot level
* For cyclic transitions states the ring size for searches can be limited to user-defined ring sizes
* Conformer search will skip going through all calculations on restart if all calculations were in place already to speed up the run
* Error detection of ab initio calculation is improved
* Many typos and small bugs are fixed, code is cleaned up in many parts

We continue our quest to fix bugs and improve the stability of the code.
- We can detect the change in point chirality during a conformer search, and such structures are ignored, i.e., the chilarility is conserved on the PES. Note that we do not yet have the ability to search for both handed cases, the one that is found is random.
- We fixed the number of conformer searches, so the limit prescribed by the user is actually respected, even for cyclic compounds.
- Created better estimates for the number of conformers for cycles.
- Some exceptions for multiplicity were fixed.
- Added an H2 elimination family
- Homolytic scissions are at feature parity with other families for the most part

We made several improvements
* more stable filtering of identical bimolecular products
* possibility of skipping wells in the search
* possibility of skipping reaction families
* improved reaction search for cycles
* reaction families are using functions (in progress still) for geometry modifications
* small bug fixes and improvements

We have improved the code and eliminated several bugs:
- hindered rotor failures are handled without crash
- `mess` files contain all channels
- in a `pes` calculations maintain central repos for wells, saving some cpu time
- new reaction family added: `beta_delta`
- several small bug fixes