Kinbot

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.

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