eljost/pysisyphus 0.4.2

• Main Author: Eljost
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: Zenodo 2020
• Subjects: Josephine; Orca
• Online Access: https://dx.doi.org/10.5281/zenodo.3910763; https://zenodo.org/record/3910763

Deprecated "opt_ends" option in "irc" section. This is now handled in the "endopt" section. Addition 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 Bugfixes 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 Miscellaneous Unified Hessian attributes in IRC integrators that use Hessians Deprecated old code Dropped dependencies: attrs, pandas, pytest-harvest Updated plotting documentation