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

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.

• 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.
• Flexible optimizer LayerOpt (type: layers in YAML input), tailored to optimize multilayer-systems, e.g., in ONIOM calculations
• Started to work on supporting rate calculations in pysisyphus, including simple tunnel corrections. See get_rates_for_geoms() and render_rx_rates() indrivers/rates.py.
• Extrapolation (before and after) a given set of geometries (see pysistrj --help | grep extrapol)
• --kcal flag in pysisplot to output energies in kcal mol⁻¹ instead of kJ mol⁻¹. Implemeting this was probably a bad idea and it may be removed again in future versions, because I really don't like cal :)
• Support for .mol2 inputs. Currently, the order "@<TRIPOS>MOLECULE and @<TRIPOS>ATOM is expected.

• Fixed energy/forces-mixing in EnergyMin calculator (see 10.1063/5.0021923)
• climb_lanczos is now supported by all subclasses of ChainOfStates, e.g., NEB. Previously it was restricted to GrowingString. By enabling it, the lowest curvature mode will be determined using the Lanczos algorithm on all climbing images. The lowest curvature will be used instead of the regular tangent.
• Improved plot appearance in pysisplot --cosforces
• Enabled cartesian coordinate system for COS optimizations
• Take CG steps if possible, while growing a string. Previously only SD steps were taken while growing.
• Fixed many Sphinx-warnings while generating the documentation
• Convergence thresholds/targets are now reported in optimizations and IRC integrations. Fixes #196.

• Added two AFIR examples: examples/opt/23_orca_afir and examples/opt/24_xtb_three_frag_afir
• Documented AFIR calculator