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qcscine/puffin: Release 2.0.0

Authors: Bensberg, Moritz; Brunken, Christoph; Csizi, Katja-Sophia; Grimmel, Stephanie A.; Gugler, Stefan; Sobez, Jan-Grimo; Steiner, Miguel; +4 Authors

qcscine/puffin: Release 2.0.0

Abstract

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.

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