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).