v0.5.0

What's Changed

Taken from CHANGELOG.md. Categorization according to Keep a Changelog.

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).

Merged Pull Requests

• Include PyPi installation into README.md and re-structure it by @marcelmbn in #41
• Make scaling factor for van-der-Waals radii for fragment detection adjustable by @marcelmbn in #45
• Add support for the new "g-xTB" method (working title: GP3-xTB) and minor bug fixes by @marcelmbn in #49
• Implemented the van der Waals radii inside the check distance function by @jonathan-schoeps in #51
• A new function to contract the coordinates after the random generation to ensure that the atoms are not to far apart. by @jonathan-schoeps in #53
• An update in the ReadMe.md to be more specific with the element composition function. by @jonathan-schoeps in #58
• Changed the uhf value when xtb calculates with lanthanides by @jonathan-schoeps in #60
• Elements 87 to 103 are now accessible via the element composition by @jonathan-schoeps in #62
• Bunch of technical fixes by @marcelmbn in #65
• Fix bug with Lr leading to an by @marcelmbn in #69
• Update Docs by @marcelmbn in #72
• Fix random number generation by removing legacy random number generation by @marcelmbn in #78
• Remove deprecated tests that are not strictly true by @marcelmbn in #79
• A fixed molecular charge for the molecule generation. by @jonathan-schoeps in #73
• atlist to ati and back conversion by @marcelmbn in #81
• Bug fix were uhf was always 0 if a fixed charge were given by @jonathan-schoeps in #80
• Update CODEOWNERS by @marcelmbn in #82
• The .UHF file is now written if the molecule has a uhf larger than 0 by @jonathan-schoeps in #74
• CHANGELOG.md fixed for previous commit by @marcelmbn in #83
• Remove dummy code by @marcelmbn in #85
• Add example for usage of Python API by @marcelmbn in #87
• Update citation and include Python 3.13 into CI by @marcelmbn in #94
• Random integer in element_composition range by @marcelmbn in #97
• Full pythonization of element_composition and forbidden_elements by @marcelmbn in #98
• fixed_composition feature by @marcelmbn in #95
• update CHANGELOG.md for commits 433bcff and b570b62 by @marcelmbn in #99

Full Changelog: v0.4.0...v0.5.0