Firecode

- renamed python_functions.py to numba_functions.py
- Decreased compenetration check threshold for close contacts to 0.5 A from 0.95 A. In this way, topological mistakes made by GFN-FF, that bind hydrogen atoms (d~0.89 A) will not automatically flag the structures as compenetrated, as this will most likely optimize fine when the theory level is raised to GFN2 or other.

- Changed library versions

- Changed numpy version to 1.20.3
- Added saturation check

- Various small bugfixes/graphic restyling
- Stuctures are optimized at embedder.options.theory_level before running the mtd_search> operator, and a FatalError is raised if they scramble during this process. This increases the robustness of the workflow by avoiding changes in the molecular graph if the input structure is bad.
- Added a warning printout system to the Embedder class, via logging and appending strings to the embedder.warnings list.
- Added a saturation and compenetration check for input molecules, that warns about potential bad geometries.

- 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).