Revamped Growing String Method

Addition

• Added parsers for cjson (as produced by Avogadro) and Z-Matrix
• (L)-BFGS with double damping
• rms_force_only argument for Optimizers to use only rms(forces) for checking convergence
• Reworked GSM implementation
  • Enabled Climbing Image
  • GSM reparametrization is much more robust
  • Added L-BFGS to StringOptimizer (with double damping)
  • DLC recreation can now be toggled
  • Energy-weighted parametrization for increased density around the Highest Energy Image
  • Upwinding tangents are used throughout, except for the frontier nodes
  • Per-Image coordinate scaling can be used in StringOptimizer
• Added new geom: block to the YAML input
• Optimization convergence can now be signalled by the operator by creating a converged file
• Added more safeguards to run_tsopt_from_cos w.r.t. selecting the initial root to follow
• Added mem argument to XTB calculator. Enabled GFN-FF

Bugfixes

• HDF5 files in optimizations are now opened/closed in every cycle, instead of keeping them open all the time.
• Present comment was ignored in Geometry.as_xyz()
• String has to be fully grown to indicate convergence
• HEI splining was faulty
• Present Hessian at optimized TS was not carried over to IRC calculation but it was recalculated (costly)

Miscellaneous

• Improved logging in L-BFGS optimizations