Pysisyphus

Small post release containing several fixes for the nix-CI running on gitlab. This release includes no functional changes.

Deprecations and Breaking Changes
- Entries for Gaussian-related utilities (`formchk`, `unfchk`, `rwfdump`) in `.pysisyphusrc` must be updated. Please see [the documentation](https://pysisyphus.readthedocs.io/en/latest/installation.html#setting-up-pysisyphusrc). For the above mentioned commands the trailing `_cmd` has been dropped (`fchk_cmd=[path to fchk]` is now only `fchk=[path to fchk]`). Alternatively, if the binaries are available on `$PATH` they should be found automatically by pysisyphus and their addition to `.pysisyphusrc` is not required. Whether the binaries are found is easily checked by executing `pysisrc` on the command line.

Addition
- Ability to dump calculations results to JSON (provide `dump: true` to calculator in YAML input)
- Remote calculator to execute calculations on external machines using `Fabric`
- `pysisreplace` entry point to substitute atoms in existing geometries with new residues, e.g, OEt, OMe or Ph. Idea from [10.1002/wcms.1510](https://wires.onlinelibrary.wiley.com/doi/epdf/10.1002/wcms.1510)
- `pysisrc` entry point to check available software and to generate a proper `.pysisyphusrc`
- An additional block can be given in `barrier` block for calculation of solvated energies (see `examples/complex/08_trispericyclic`)
- `scripts/aciddrain.py` for batch calculation of pKa-values using [luigi](https://luigi.readthedocs.io/en/stable/) and [LFER](https://pubs.acs.org/doi/abs/10.1021/acs.jpca.1c03463) fitting (linear free energy relationship)
- `EnergyMin` calculator to optimize to allow, e.g., different multiplicities along a COS, see [10.1063/5.0021923](https://doi.org/10.1063/5.0021923)
- Methods to center and randomly rotate geometries (`Geometry.center()` and `Geometry.rotate()`)
- Formed/broken bonds are now reported along an IRC integration

Bugfixes & Improvements
- TDEN overlaps are much faster
- Fixed several deprecation warnings
- Update Github action workflows
- Improved integration with [thermoanalysis](https://github.com/eljost/thermoanalysis) and fixed calculation of wavenumbers of normal modes
- Amound of requested memory is now checked and adjusted if too much was requested
- `endopt` can now be requested without previous IRC run
- Gathered more global configuration values in `config.py`, e.g., default temperature and pressure, default sub-directory to store external QC program logs
- Disabled long running tests in CI to save time in the test suite
- sheepforce updated nix-related files
- Parsing of TURBOMOLE Hessians for bigger systems was faulty (fixes 173)

Miscellaneous
- QC-logfiles etc. are now dumped to `qm_calcs` subdirectory
- Christmas themed logo for next christmas season ;)
- Tighted default `overachieve_factor` to `5`
- Switched from `setup.py` to `setup.cfg` and `pyproject.toml`

Deprecations and Breaking Changes
- Entries for Gaussian-related utilities (`formchk`, `unfchk`, `rwfdump`) in `.pysisyphusrc` must be updated. Please see [the documentation](https://pysisyphus.readthedocs.io/en/latest/installation.html#setting-up-pysisyphusrc). For the above mentioned commands the trailing `_cmd` has been dropped (`fchk_cmd=[path to fchk]` is now only `fchk=[path to fchk]`). Alternatively, if the binaries are available on `$PATH` they should be found automatically by pysisyphus and their addition to `.pysisyphusrc` is not required. Whether the binaries are found is easily checked by executing `pysisrc` on the command line.

Addition
- Calculator for Conical intersection optimization (`type: conical`), implementing the [updated branching plane](https://pubs.acs.org/doi/10.1021/ct1000268) algorithm. See `examples/opt/17_orca_conical_intersection`.
- Simple [ursina](https://www.ursinaengine.org/)-based script that can read and visualize pysisyphus HDF5 Hessians to animate imaginary modes (`scripts/modes3d.py`)
- Dipole moment calculation in OpenMM calculator
- New internal coordinates: BondedFragment and DummyTorsion; suitable for optimization of water interaction energies, as needed for parametrizing CGENFF.
- Alternative implementations of bends and torsions, using atan2 instead of acos, that are numerically more stable. 2nd derivatives of Torsions are now calculated using the code-generated derivatives, starting from the atan2 expression.
- Support for `exit` sign to cleanly shutdown calculations
- `perf` driver to benchmark calculation-speedups with varying `pal`
- Implemented Bofills TS-Hessian update `hessian_update: ts_bofill`
- Support for ALPB solvent in XTB calculator
- Frozen atoms can now be excluded from the internal coordinate setup algorithm (please see the [documentation](https://pysisyphus.readthedocs.io/en/latest/coordinate_systems.html#freeze-atoms))

Bugfixes
- `pr_nto` argument to OverlapCalculator was ignored
- Don't try to call thermoanalysis, when it is not installed
- IRC classes now respect `out_dir` argument
- Requesting 2nd derivative of Rotations w.r.t. Cartesian coordinates led to a crash

Miscellaneous
- Version string is now dumped to RUN.yaml
- Improved Growing-Newton-Trajectory class
- Improved printing of internal coordinates in `pysistrj --internals`
- Relaxed scans are more robust
- Speeded up some internal coordinates by avoiding calls to numpy methods
- MO-coefficients can now be set in .gbw files
- Initial dimer calculation can now be read from a HDF5 Hessian imaginary mode
- Energy change is now reported in the first column of an optimization
- Switched from plain down-scaling to shifted-Newton-step when proposed RFO-step is too big
- Interpolation in internal coordinates is now more robust

Addition
- Added ability to retry/rerun crashed calculations (`retry_calc: 1`). For now only supported by ORCA.
- Support for `fragments: total` in `endopt:` section. This allows optimizing the system as whole as well as optimizing the separate fragments
- Single geometries from multi-geometry input files can now be accessed via pythons index-notation: `fn: multi_geoms.trj[1]` would only load the second geometry from `multi_geoms.trj`
- Very basic support for [preconditioning of position and rotation](https://doi.org/10.1002/jcc.26495). `precontr:` in YAML input; runs before `preopt`. Still very slow for sizable systems.
- `pr_nto` keyword support for `OverlapCalculator` to dynamically select the number of NTO pairs in overlap calculations

Bugfixes
- Hessian was unnecessarily recalculated in TS optimizations after COS runs
- Fixed Eckart projection to remove translation and rotation. Adapted from [geomeTRIC](https://github.com/leeping/geomeTRIC/blob/master/geometric/normal_modes.py)
- Eckart projection in calculation of initial displacement from TS in IRC runs was never carried out
- Made parsing & storing of MO and CI coefficients in `store_overlap_data()` much more consistent

Miscellaneous
- coord_type in optimizations and wavenumber of imaginary mode in IRC runs is now reported
- Added separate ORCA5 calculator (`type: orca5`) so ORCA4 and ORCA5 can be setup in parallel
- Refactored geometry loading via `get_geoms` and `read_geoms` in `trj.py` to support arbitrary kwargs
- All `preopt/tsopt/endopt` sections can now contain a `geom` section, e.g., to control the coord_type
- Requested and actual energy lowering is now reported in IRC runs
- Wavenumber/frequencies are now also reported when thermoanalysis is printed