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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Added

  • Distance constraints for xTB (normalized parsing, config validation, runtime enforcement, and optional integration test).
  • Distance constrains for ORCA (uses xTB as as driver to set the same distance constrains for the postprocess).

[0.6.0] - 2025-04-01

Changed

  • to set the elemental composition it is now possible to use dicts with not only int but also the element symbols (str)
  • dict keys for elemental compositions will now always be checked for validity
  • Renamed GP3-xTB to g-xTB
  • Moved constants and (empirical) parameters to the data module
  • Default for optimization cycles in the postprocessing step set to program default (convergence)

Deprecated

  • Nothing will be printed while multiple molecules are generated in parallel, tqdm-based progress bar instead
  • Some debugging statements from generate had to be removed (esp. w.r.t. early stopping)

Added

  • GXTBConfig class for the g-xTB method, supporting SCF cycles check
  • support for TURBOMOLE as QM engine
  • updated the parallelization to work over the number of molecules
  • possibility to generate symmetrical molecules (choice from rotation, inversion, mirroring)
  • number of optimization steps in the postprocessing part can be set to program default by none
  • support for a manually defined temporary directory for the QM calculations

Fixed

  • version string is now correctly formatted and printed
  • precision (# significant digits) of the coordinate files (get_coord_str and get_xyz_str) increased from 7 to 14
  • catch encoding errors when reading Turbomole._run_opt output files
  • bug in the parallelization, leading to a dead mindlessgen execution as a consequence of not allowing the required number of cores
  • stop_event checked before every external call to avoid unnecessary executions

[0.5.0] - 2024-12-16

Changed

  • vdW radii scaling parameter can now be adjusted via mindlessgen.toml or CLI
  • check_distance function now checks based on the sum of the van der Waals radii and a scaling factor acessible via mindlessgen.toml or CLI
  • better type hints for Callables
  • clearer differentiation between the distinct scaling factors for the van der Waals radii
  • README.md with more detailed explanation of the element composition function
  • Default max_cycles for the generation & refinement set to 200
  • Allow fixed molecule compositions in a simpler way
  • check_config now ConfigClass-specific
  • modify atom list adaption to element_composition such that a random integer in the given range is taken and not the lower/upper bound

Fixed

  • unit conversion for (currenly unused) vdW radii from the original Fortran project
  • minor print output issues (no new line breaks, more consistent verbosity differentiation, ...)
  • bug in postprocess_mol which led to an unassigned return variable in the single-point case
  • bug leading to UnicodeDecodeError when reading xtb output files
  • bug with all atom lists being initialized with a length of 102 instead of 103
  • inconsistent default values for the mindlessgen.toml and the ConfigManager class
  • legacy pseudo random number generation removed and replaced by np.random.default_rng() for avoiding interference with other packages

Added

  • support for the novel "g-xTB" method (previous working title: GP3-xTB)
  • function which contracts the coordinates after the initial generation
  • function which is able to printout the xyz coordinates to the terminal similar to the .xyz layout
  • elements 87 to 103 are accessible via the element composition. If xtb is the engine, the elements will be replaced by their lighter homologues.
  • support for python-3.13
  • option to set a fixed molecular charge, while ensuring uhf = 0
  • element_composition and forbidden_elements can now be directly set to a dict or list, respectively, via API access

Breaking Changes

  • Removal of the dist_threshold flag and in the -toml file.
  • The number of unpaired electrons (Molecule.uhf) is now set to 0 if xtb is used as QMMethod and a lanthanide is within the molecule to match the f-in-core approximation.
  • "Contract Coordinates" functionality set to true by default in the mindlessgen.toml file.
  • basename.UHF and basename.CHRG are only written to disk if they differ from the default value (0 and 0, respectively).

[0.4.0] - 2024-09-19

Changed

  • Default file name of .xyz file contains prefix mlm_
  • Comment line of .xyz file contains the total charge and number of unpaired electrons
  • Default ORCA calculation changed from r2SCAN-3c to PBE/def2-SVP
  • verbosity = 3 always prints full QM output
  • Adapted generation of number of unpaired electrons; thereby, support for Ln's
  • Shifted group / element sorting definitions to miscellaneous
  • xyz files are written on the fly, and not post-generation
  • GFN-xTB level can now be set
  • mindless.molecules file is written continuously during generation

Fixed

  • test_iterative_optimization more deterministic
  • wrong atom range check in for the isomerization mode (#21)
  • forbidden_elements and element_composition influences hydrogen and organic element addition
  • more realistic default mindlessgen.toml entries

Added

  • Optimization via DFT in the post-processing step
  • Detailed input of ORCA settings (functional, basis, grid size, SCF cycles, ...) possible
  • min_num_atoms and max_num_atoms consistency check
  • Maximum number of optimization cycles are an argument for the QMMethod.optimize base function
  • Debug option for the refinement and post-processing step specifically
  • Return type for single_molecule_generator
  • Check for consistency of the min_num_atoms and max_num_atoms constraint
  • Similar to the <basename>.CHRG file, also a <basename>.UHF is printed
  • HOMO-LUMO gap check within the refinement step and corresponding Config option called "refine_hlgap"
  • GeneralConfig switch for writing xyz files
  • PyPi and TestPyPi upload of releases (new workflow)

[0.3.0] - 2024-08-20

Breaking Changes

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Added

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Changed

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Removed

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Fixed

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Deprecations

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