Kinbot

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.

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