Scine-puffin

-------------

New Jobs:
- Automatic QM region selection for QM/MM.
- Job that tries to find a new reaction starting from a transition state guess only.
- Job that carries out a fast dissociation reaction trial protocol after optimizing the input structure.
- Remove `scine_step_refinement` job.

New Settings:
- Add the option `allow_exhaustive_product_decomposition` to jobs that carry out reaction trials, which allows products to decompose and re-optimize them until no further decomposition is observed.
- Add the option `always_add_barrierless_step_for_reactive_complex` to jobs that carry out reaction trials, which enables that a barrierless elementary step is added for the reactive complex formation of a bimolecular reaction irrespective of the complexation energy.
- Add option `store_structures_with_frequency` and `store_structures_with_fraction` that allow storing a portion of structures per sub-task.
- Add option `spin_propensity_ts_check` to `scine_react_ts_guess` job to specify a spin multiplicity range to be checked for the transition state different to the spin multiplicity range to be checked for the reactants and products (`spin_propensity_check`)

Technical changes:
- Ensure that the calculated spin states are considered in the calculation of the dissociation energy in the `DissociationCut` jobs and in structure optimizing jobs (`GeometryOptimization` and `ReactTsGuess`)
- Write normalized modes in database.
- Improve dependency handling and add more typehints.
- Optimize only unique structures of the endpoints of an IRC calculation.
- Deduplicate code for analyzing both sides of the IRC part in the `scine_react_job`.
- Stricter conditions to distribute charges if `expect_charge_separation` is set to `True` by prohibiting changing
already changed charge.
- Comply docstrings with numpy styling.
- Introduce Enums for ReaDuct calls.

-------------

New Features:
- Store found elementary step even if none of the endpoints corresponds to the initial starting structures
- Add restart information with valid TS for jobs trying to find new elementary steps, where the IRC failed to produce different endpoints
- Consider potential surface structures for label determination of new structures
- Logic to transfer indices information and other complex properties from reactants to products
- Save close lying spin multiplicities and allow to manipulate exact spin propensity
check behavior with added settings

New Jobs:
- Microkinetic modeling with the program Reaction Mechanism Simulator.

New interfaced programs
- AMS via SCINE AMS Wrapper
- MRCC (release version March 2022)

Bug fixes:
- Ensure that `only_distance_connectivity` is adhered in all reaction jobs

Other:
- Update address in license

-------------

New Features:
- Add a mechanism to stop multiple Puffins
- Generate PID based on UUID, allowing to run multiple Puffins on the same filesystem

New Jobs:
- Double ended reaction step refinement.

Further changes:
- Various bugfixes and improvements

-------------

New Features:
- Support for stable intermediate complexes and barrier-less reactions
- Strongly interacting complexes containing multiple structures
are now saved in the database.
- Spontaneous barrier-less associations detected during reaction probing
are now considered barrier-less reactions.
- Uphill barrier-less dissociations may be probed.
- All structures visited during reaction probing may be saved in the
database if required.

New Jobs:
- Open source (SCINE-based) jobs
- Elementary step refinement starting from a previously optimized transition state
- Conceptual DFT property calculation
- QM/MM force calculation
- Barrier-less dissociation probing

- New interfaced programs
- SCINE Swoose

-------------

Initial Features:
- Runs as a daemon
- With possible graceful timeout/shutdown after a user-defined time
- With automatic cleaning of failed jobs
- With a tolerance for database disconnects at the end of jobs
- Provides a containerized version
- Usable with Docker, Podman, and Singularity
- Includes/installs all open source programs

Initial Jobs:
- Open source (SCINE-based) jobs
- Conformer generation
- Artificial force induced reactions (AFIR) optimization
- Bond order generation
- Geometry optimization
- Hessian generation incl. thermo chemistry
- IRC scan
- Reactive complex reaction probing (using AFIR, NT1, NT2)
- Single point calculations
- Transition state optimization

- Specialized jobs:
- Gaussian: partial charges - charge model 5 (CM5)
- Orca: geometry optimization
- Turbomole: geometry optimization
- Turbomole: single point
- Turbomole: Hessian
- RDKit: conformer generation

Initially interfaced programs used in calculations:
- SCINE Molassembler
- SCINE Readuct
- SCINE Sparrow
- Serenity (v1.4, via SCINE Serenity Wrapper)
- XTB (v6.4.1, via SCINE XTB Wrapper)
- Orca (v4.1.X, v4.2.X)
- Turbomole (v7.x.x)
- Gaussian (g09 Rev. D.01)