Release 2.0.0

Changes:

• 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.
• 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)
• 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.

Release 1.3.0

Changes:
- 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
- Microkinetic modeling with the program Reaction Mechanism Simulator.
- AMS via SCINE AMS Wrapper
- MRCC (release version March 2022)
- Ensure that only_distance_connectivity is adhered in all reaction jobs
- Update address in license

Release 1.2.0

Changes:
- Add a mechanism to stop multiple Puffins
- Generate PID based on UUID, allowing to run multiple Puffins on the same filesystem
- Double ended reaction step refinement.
- Various bugfixes and improvements

Release 1.1.0

Changes:

• 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:

  • 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

Release 1.0.0

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)