eljost/pysisyphus 0.4.2

Deprecated

• "opt_ends" option in "irc" section. This is now handled in the "endopt" section.

• Analytical Rastrigin function with many local minima
• Updated stocastic search code & added tests
• Very simple and barebones PDB parser & writer
• Ability to omit Link atoms in ONIOM
• ONIOM Hessian
• ONIOM gradient & Hessian are now calculated using a Jacobian, which simplifies the code
• Enabled ONIOM for YAML input
• Added support for fragments and simple selection by regular expressions to Geometry
• Optimizer data is not dumped to YAML anymore, but written to separate HDF5 groups, which is way way faster
• Calculated Hessians from optimizations/IRCs are now dumped into a more useful HDF5 file with additional information. The file can easily be used as input for the "thermoanalysis" software to calculate thermochemical corrections (G, H, S, etc.)
• Imaginary frequencies (< -10 cm⁻¹) after final hessian calculation are now written to .trj for easy inspection
• Location of .pysisyphusrc can now be read from PYSISRC environment variable
• Added thin packmol wrapper (pysispack) for easy creation of initial MD configurations
• MD related functionality now operates in sane units
• Initial GFN1-XTB hessian for (TS)-optimizations using different calculators
• Simple intial Hessians for cartesian geometries through back-transformation of internal coordinate model Hessians
• NumFreq can now be requested for ORCA calculator
• Added "endopt" section (simlar to "preopt") to configure optimizations started from IRC endpoints
• Josephine

• overachieve_factor is now also respected with "baker" thresh
• Definition of dihedrals in rings
• Multistep jobs (preopt, opt, tsopt) lead to overwritten yaml dumps. This is now fixed.
• Simplified/unified plotting of COS methods (cosens/cosforces)
• Unit conversion for inline xyz coordinates
• Sometimes the last IRC points were not dumped to HDF5

• Unified Hessian attributes in IRC integrators that use Hessians
• Deprecated old code
• Dropped dependencies: attrs, pandas, pytest-harvest
• Updated plotting documentation