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Release 4.0.0

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@weymutht weymutht released this 26 Aug 04:31

Changes:

  • Move network refinement to separate folder
  • Move all filters to separate folder
  • Move reaction rules to separate folder
  • Remove deprecated database queries
  • Removed some gear options such as pre_refine_model in favor of the default model field
  • Set the default model option with PlaceHolderModel and check if it is still present before launching the gear to make sure that an intended model is used
  • Small changes to the default arguments of the kinetic modeling gear to facilitate its use in SCINE Heron
  • Add StructureFilters derived from fitting AggregatesFilters.
  • Assemble reactive complexes from two given molecules easily with an CLI.
  • Elementary Step Gears can set up reaction trials for flasks.
  • Almost all Aggregate and ReactiveSiteFilters are made suitable for flasks. If not, a note is included in the documentation.
  • Add an AggregateFilter that filters based on substructure searches.
  • Add an AggregateFilter that filters based on allowed / disallowed molecular charges.
  • Add reverse option for some existing AggregateFilters.
  • KineticsGear now has an option that allows to run it as many cycles as long as no new aggregates are activated and then stops itself.
  • Add gear to carry out additional energy calculations.
  • Kinetic modeling may now work with a mixture of electronic structure models.
  • Energies may now be automatically referenced as formation energies from the atoms.
  • The bond-based trial generator is now able to enable (enable exploration/analysis) the analysis of structures,
    elementary steps, etc. in the results of already completed calculations, i.e., the trial generator detects that
    it already set up a calculation previously. Instead of just continuing, it may then enable the results of this
    calculation. This simulates a step-wise exploration of already existing data in the DB that was disabled before
    and is intended to allow re-exploration with different reaction conditions such as temperature and pressure or
    recycle existing data after changing the kinetics gear (or kinetic modeling, pathfinder etc.).
  • Add a framework to filter reactions (analogous to the aggregates filters) and filter elementary steps. These
    new filters can be applied to the refinement framework (e.g., barrier-screening, barrier-less reaction selection,
    concentrations etc.).
  • The refinement is now split into 3 gears:
    • Calculation-based refinement looping over the calculations and refining elementary steps (structures etc).
    • Reaction-based refinement looping over reactions and selects elementary steps to be refined for each reaction
      (including energy window for the step selection).
    • Aggregate-based refinement looping over aggregates and refining the structures of these aggregates (including
      energy window for the selection of the structure).
  • All refinement gears support the same enabling strategy as introduced to the bond-based trial generator.
  • Add reaction filter-based kinetics gear.
  • Add reaction filter to constrain the maximum energy encountered when exploring a single potential energy surface.
  • Add an aggregate filter to enforce that the particle number is conserved during the exploration.
  • Add feature that a running Network Expansion of the Steering Wheel can be interrupted and continued later.
  • Rework the Engine / Gear interaction, by replacing the sent signals with shared memory members
  • Add EngineHandler class to join any forked engines if a signal is sent, replacing the custom code in the main script; the class also allows for running all engines and stopping the processes gracefully
  • Change the internal representation of some AggregateFilters from strings to enums in order to be faster.
  • Add additional caches to some AggregateFilters for increased performance.
  • Add more default settings.
  • The MinimalConnectivityKinetics and BasicBarrierHeightKinetics did not consider reactions where all reactants on the right hand side were available, which lead to fewer activated aggregates
  • GearOptions of the NetworkExpansion did not consider that there could be multiple gears of the same type but with different options in a protocol, hence their datastructure (including access keys) are now changed.
  • Fix type annotations in the documentation.
  • get_transition_state_free_energy in the reaction_wrapper now returns max(e_lhs, e_rhs) if the reaction is
    barrier-less.
  • Add more typehints