Tscode

- Reduced/summarized printouts for loose to tight optimization steps.
<!-- - Removed call to compenetration_refining() on input ensemble: it is usually already pruned for compenetration for embed runs, and other ensembles (for example from "refine> mtd>" runs coming from CREST) benefit from relaxing eventual clashes that are present. -->

- CREST constraints (mtd_search>) are now passed as distance constraints instead of atom fixing (forgot to implement it this way before?).
- CREST metadynamics input/output files are all retained now and not deleted after execution.
- Output names changed from starting with "TSCoDe" to "tscode" for easier typing.
- Modified variable definition of periodic table in tscode.pt to avoid ValueError(s).
- Added the mep_relax> operator (beta, not present in documentation) to relax chains of images along the PES. Useful to get good starting points for higher-level NEB calculations. First, the optimization is performed by retaining all bond distances, which are then relaxed after the first cycle is converged (developed to find atropisomer interconversion pathways).

- Updated library dependency versions.

- Restyled copy of input in the log file.
- Added citations to the main program and external modules if they are used (references.py, embedder.py/_print_references).
- In runs with operators, t_start_run is set before running the first operator, and it is not overwritten by RunEmbedding if it was already set. This makes sure that the final time always includes the time spent executing the operators.

- CRESTNCI keyword: passes "--nci" to CREST, making it run in "NCI mode" that is applying a wall potential to prevent unconstrained non-covalent complexes from evaporating during the dynamics.
- If metadynamic conformational searches fail (CalledProcessError) at the default GFN2-XTB//GFN-FF level they are re-launched with pure GFN2-XTB (slower but more stable and works with inorganic ions).

- Added support for passing an energy threshold to mtd_search> CREST runs ("--ewin" in CREST, set with the KCAL keyword on TSCoDe).
- Dynamically adjusted energy pruning threshold above self.options.kcal_thresh in optimization_refining if needed, so that at least a percentage of structures is retained (default minimum set to 10%).