eljost/pysisyphus: Bugfixes, Refactoring for more consistency ...

• Main Authors: Steinmetzer, Johannes, , Phillip, Jones, Greg, Ms860309
• Format: Software
• Language: unknown
• Published: Zenodo 2021
• Subjects: Orca
• Online Access: https://dx.doi.org/10.5281/zenodo.5497269; https://zenodo.org/record/5497269

Addition Added ability to retry/rerun crashed calculations ( retry_calc: 1 ). For now only supported by ORCA. Support for fragments: total in endopt: section. This allows optimizing the system as whole as well as optimizing the separate fragments Single geometries from multi-geometry input files can now be accessed via pythons index-notation: fn: multi_geoms.trj[1] would only load the second geometry from multi_geoms.trj Very basic support for preconditioning of position and rotation. precontr: in YAML input; runs before preopt . Still very slow for sizable systems. pr_nto keyword support for OverlapCalculator to dynamically select the number of NTO pairs in overlap calculations Bugfixes Hessian was unnecessarily recalculated in TS optimizations after COS runs Fixed Eckart projection to remove translation and rotation. Adapted from geomeTRIC Eckart projection in calculation of initial displacement from TS in IRC runs was never carried out Made parsing & storing of MO and CI coefficients in ...