eljost/pysisyphus: ONIOM optimization, AFIR improvements, New coordinate systems ...

• Main Authors: Steinmetzer, Johannes, , Phillip, Jones, Greg, Ms860309
• Format: Software
• Language: unknown
• Published: Zenodo 2022
• Subjects: Lagrange; Orca
• Online Access: https://dx.doi.org/10.5281/zenodo.6513774; https://zenodo.org/record/6513774

Deprecations, Breaking Changes Updated handling of coordinate rebuilding. Previously, only the invalid coordinates (bends close to being linear, torsions with (nearly) collinear atoms) were dropped and no new coordinates were determined. Now a new set of coordinates is determined for the given coordinates and used in conjunction with the remaining valid coordinates. Addition Support for nix flakes, provided by @sheepforce AFIR-Hessian scripts/orca2cdd.py for simple CDD-cube generation with Multiwfn from ORCA .cis and .gbw files New coordinate systems: hredund and hdlc that also contain the atomic Cartesian coordinates in addition to the regular set of internals. Also cartesian and mwcartesian which will eventually supersede cart . The former coordinate systems implement the CoordSys protocol and should be more future-proof, e.g., with them Cartesian constraints using Lagrange multipliers could be implemented. See the commit message of c2a901b22828df20dbef1acc33fd1a78d0be7e61 for a more thorough discussion. ...