v0.4.0

What's changed

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)

Merged pull requests

• Create more guidelines and update README.md links by @marcelmbn in #8
• Fix markdown typos by @marcelmbn in #9
• xyz file changes and more DFT options in post-processing by @marcelmbn in #10
• Change default basis set to def2-SVP by @marcelmbn in #11
• Exclude mindlessgen.toml from CI by @marcelmbn in #12
• Enable debugging of post-processing step explicitly by @marcelmbn in #14
• Check for consistency of the min/max constraint of the number of atoms by @marcelmbn in #15
• add Ln support by adaptive UHF recognition by @marcelmbn in #16
• Enhance documentation and code style by @marcelmbn in #20
• Fix bug in isomerization mode that doesn't allow giving the exact atom number by @marcelmbn in #21
• Include one-pager by @marcelmbn in #22
• Re-introduce HOMO-LUMO gap check by @marcelmbn in #25
• Better defaults, config description and CI check skips by @marcelmbn in #28
• Continuous xyz file writing by @marcelmbn in #29
• Bug fix: Hydrogen and organic elements were ignored by the forbidden_elements by @marcelmbn in #31
• Fix test_iterative_optimization by @marcelmbn in #32
• introduce more general fragmentation test by @marcelmbn in #34
• GFN level now accessible by @jonathan-schoeps in #35
• Append to 'mindless.molecules' and better printout per molecule by @marcelmbn in #37
• Add release workflow by @marcelmbn in #38
• Make release.yml more consistent by @marcelmbn in #39
• Prepare v0.4.0 release by @marcelmbn in #40

New Contributors

• @marcelmbn made their first contribution in #8
• @jonathan-schoeps made their first contribution in #35

Full Changelog: v0.3.0...v0.4.0