Kinbot

**Full Changelog**: https://github.com/zadorlab/KinBot/compare/2.2.3...2.2.4

**Full Changelog**: https://github.com/zadorlab/KinBot/compare/2.2.4...2.2.4a

**Full Changelog**: https://github.com/zadorlab/KinBot/compare/2.2.2...2.2.3

What's Changed

General features

* Optimization can be carried out with the performant [Sella](https://github.com/zadorlab/sella) optimizer and also allowing the code to be used with any ASE calculator
* A rewrite of some parts of the `reaction_generator` where it deals with product generation
* Increasing robustness when many conformers fail, especially when the first one, which can happen a lot for cations
* Differentiated thresholds for barrierless reactions and between L1 and L2
* Allow TS to have a second imaginary frequency smaller than imagfreq_threshold parameter, also when comparing L2 to L1
* H2 elimination family is extended
* Rigid distance cutoff for reaction search is a parameter now
* Fallback values for bondlength thresholds

Ions

* Handling of cations is improved, especially cation fragments

van der Waals wells

* Automatic detection using IRC product energies
* Writing vdW to PESViewer input

Cluster mode

* Allowing certain calculations on clusters of molecules
* Detection of hydrogen bonds

VRC-TST

* 1-D relaxed scan of bonds is implemented with corresponding "high" level of energy evaluations
* 1-D rigid scans matching the relaxed one is implemented with corresponding "sample" level of energy evaluations
* [Sella](https://github.com/zadorlab/sella)-driven optimization of scans, including the prevention of fragment flips for symmetrically equivalent or chemically alternate cases (e.g., resonance stabilization)
* Automatic placement of pivot points, even when geometrical hints are absent
* Visualization of correction potential
* Input writing for VRC-TST code

Some bug fixes

* Symmetric bond scission's occasional bug
* Enabling clean end on single well case in `pes` mode
* Ozone has correct multiplicity

Improvements:
* Use Sella as an optimizer allowing to use KinBot with any ase calculator.
* Allow running calculationss with ions (beta).
* Added new reaction family 'Intra_disproportionation'.
* Added new reaction family 'bimolec_disproportionation'.
* Enable the keep_chemids option to run kinbot only on specific species.
* Added the possibility to have method-specific queue templates.
* Allow the user to define the minimum negative frequency to accept as valid.
* Allow the user to define the threshold for a ring to be considered as flat.
* Added fallback value for bond length cutoff when the value is not hard coded.
* Improved the information displayed in kinbot.log file.
* Implemented a factory function to create StationaryPoint objects from an ase.Atoms object.
* Improved the filtering of different structures in homolytic scissions.
* Improved the identification of correct/incorrect jobs through advanced frequency analysis.
* Increase the general robustness of the code.
* Allow pes command to be run on mac computers.
* Updated examples.
* Updated README.

Bug fixes:
* Fixed bug with ZPE in L1 energies for conformers, species without them and correctly pick the lowest one.
* Fixed identification of unique conformers in multiconformer TST.
* Fixed bug with reactions tagged under skipped_reactions not being skipped.
* Fixed bug with duplicated frequencies when trying to correct failed calculations.
* Fixed bug with diverging IRC calculations.
* Fixed bug in IRC products.
* Fixed bug in energies for homolytic scissions.
* Fixed bug when computing statistics about L2-L3 energy differences.
* Fixed wrong db entry when reading the Hessian.
* Fixed bug for the identification of .com files.
* Fixed bug in barrierless reactions when generating the pesviewer input file.
* Fixed the LOT information written in MESS input files.
* Add memory specification in slurm template.
* Fixed errors when running in local mode.

Improvements:
* Improved the behavior of the kinbot.log file:
* When a new execution of kinbot/pes is carried out, former log files are backed up by renaming them to the date of their execution.
* A timestamp is added to each logging event.
* Include warnings and exceptions ocurring during execution.
* Made a conda-forge package to installation via conda.
* Increased the robustness of the function to calculate L3-L2 difference and improved the output of information.
* Improved information provided by the T1 diagnostics analysis.
* Refactored code to include tpl and reaction directories inside kinbot.
* Remove the use of pkg_resources.
* Make a safety check on the initial geometry for increased robustness.
* Improved all examples and added a new one where the molecule is specified via the structure keyword and xyz coordinates.
* Updated README.

Bug fixes:
* Fixed error with molpro sbatch file.
* Fixed bug with homolytic scissions.
* Fixed bug when dealing with MESS input files for reactions with barrieless reactions.
* Fixed errors when running in local mode.