Pysisyphus

Addition
- [DFTB+](https://dftbplus.org/) 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](https://github.com/eljost/pysisyphus/tree/master/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](https://github.com/grimme-lab/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](https://cachix.org/) and sheepforce. See the [documentation](https://pysisyphus.readthedocs.io/en/latest/nix.html#binary-caching) 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](https://scikit-learn.org/) dependency, as the new bond detection uses a [KD-Tree](https://de.wikipedia.org/wiki/K-d-Baum)
- Updated GS2 IRC integrator

Addition
- Linesearch in min and max subspaces for RSPRFO (disabled be default). Use `min_line_search: True`, `max_line_search: True` to enable it
- AFIR enhancments:
- Support for arbitrary number of fragments
- Different rhos (push/pull) and gammas can now be specified for every fragment pair
- Hydrogens are ignored by default. Use `ignore_hydrogen: False` to enable AFIR forces on hydrogens
- `pysistrj [input] --topdb` converts geometries to PDB with automated fragment detection
- `quiet` mode for XTB calculator (prevents creation of log files etc.)
- Enabled [minimum dynamic path](https://doi.org/10.1063/1.5082885) from YAML input (still undocumented, see `examples/mdp/01_trispericyclic)
- `run_tsopt_from_cos` now supports `coord_type: cart|dlc` (default dlc)
- Basic test suite that ships with a pysisyphus installation (execut with `pytest --pyargs pysisyphus.tests -v`)
- Enabled QCEngine calculator from YAML input
- On-the-fly internal coordinate rebuilding for GrowingString
- After endopt not only RMSDs are compared, but also bond matrices, making it easier to judge if a COS/TSOpt/IRC/EndOpt run was successful
- Basic Dalton calculator using `daltonproject` (energies & gradient)
- MO re-normalization for TDEN overlaps when AO overlaps are reconstructed from MO coefficients (disabled by default, use `mo_renorm: True`)
- Ability to select which set of MO coefficients (reference/current) is used to recover AO overlaps (default cur, use `mos_ref: cur|ref`)

Bugfixes
- Nix build of wfoverlap failed
- Disabled Eckart projection in hessian saving of analytical potentials
- Orthogonal direction for LinearBend and LinearDisplacement is now kept throughout the lifetime of the coordinate
- Allow `pysis [yaml] --cp [dest]` to be run outside the dir `[yaml]` resides in
- Dihedral generation in situations with 4 collinear atoms
- Generation of 3N-6 DLCs is now enforced
- More reasonable threshold for inverting WIlson B-matrix (1e-7 for eigenvalues of G matrix, corresponding to 3.16e-4 for singular values)

Miscellaneous
- No more "hand-coded" constants, now the `scipy.constants` package is used
- Double damping is now enabled by default in StringOptimizer (`double_damp: true`)

Addition
- Installation of pysisyphus & dependencies like QC codes using Nix thanks to sheepforce
- DLC coordinate weighting
- On-the-fly primitive coordinate rebuilding if the current set becomes invalid/ill-defined
- Arbitrary precision calculation of internal derivatives using mpmath
- Revamped RFOptimizer
- Added second type for linear bends (LinearDisplacement) and OutOfPlane coordinate (both are not used yet)
- RMSDs and barrier heights are now reported after "endopt" runs if possible

Bugfixes
- Generated derivatives for dihedrals fail at 0° and 180° ... disabled them for now
- pinv is now used with proper rcond value ...

Miscellaneous
- Removed redund_v2. LinearBends are now used by default if necessary
- Primitive internal setup & update was moved outside the RedundantCoord class into separate function, which should facilitate reuse
- Generated code for primitives is now verified against finite differences

Addition
- Added parsers for cjson (as produced by Avogadro) and Z-Matrix
- (L)-BFGS with [double damping](https://arxiv.org/abs/2006.08877)
- 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](https://onlinelibrary.wiley.com/doi/full/10.1002/ange.202004239)

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

- Multiwfn calls are now logged
- Default commands are used when checking for the availability of software (Multiwfn, Jmol, ...)
- Added TD-DFT optimization example using ORCA

Addition
- TIP3P water calculator
- Restricted Step Algorithm (RSA) for geometry optimizations
- Reference to pysisyphus-paper; corresponding BibTex entry is display by `pysis --bibtex`
- HDF5 Hessian dump after "do_hess: True"

Bugfixes
- Made OverlapCalculator (hopefully) more robust
- Multiwfn (MWFN) crashes shouldn't crash pysisyphus anymore
- After MWFN crash subsequent MWFN calls are avoided/disabled
- Proper fallbacks for the "cdds" argument are used when MWFN and/or Jmol are not available

Miscellaneous
- Started to add basic MD functionality (constraints via RATTLE, thermostating via CSVR) but this won't be ready anytime soon