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.

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:

New interfaced programs

Bug fixes:

Other:

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:

Further changes:

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:

Initially interfaced programs used in calculations: