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DFTB+ calculator, Davidson algorithm, Preconditioner improvements, faster Nix installation

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@eljost eljost released this 10 Nov 13:33
ae32285

Addition

  • DFTB+ calculator that supports ES tracking
  • Davidson algorithm to converge normal modes after TS optimization. Allows verifying the nature/order of the saddle point, without explicit Hessian calculation (do_davidson: True). See examples/tsopt/04_diels_alder_xtb_tsopt_davidson for an example.
  • New, faster algorithms to detect bonds and bends in large(r) systems. Dihedral detection is yet to be updated and still slow for big systems.
  • More finegrained control over preconditioner construction, selectable via kind: full|full_fast|bonds_bends|bonds
    • full/full_fast: Use bonds, bends, dihedrals
    • bonds_bends: Use bonds and bends
    • bonds: Only bonds.
  • Preconditioner construction was vastly accelerated.
  • Backtracking line search that also uses gradient information. Useful for XTB calculations, as the gradient is always available with the energy
  • Support for (re)using GFN-FF topology files in the XTB calculator
  • Nix installation using cached binaries, thanks to Cachix and @sheepforce. See the documentation on how to set up binary caching.

Bugfixes

  • Updated code to work with recently released h5py 3.0.0
  • pysisplot -o crash when no rendered CDDs were available
  • Handling of TS-optimization after COS optimization when HEI is first or last image
  • Line search now checks for very small alphas and aborts if necessary

Miscellaneous

  • Added scikit-learn dependency, as the new bond detection uses a KD-Tree
  • Updated GS2 IRC integrator