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CHANGELOG.rst

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Changelog

Release 2.0.0

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.

Release 1.3.0

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

Release 1.2.0

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

Release 1.1.0

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

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)