Merge changes from `sync_dimer` branch

[ireaml]

Changes:

1. Enable user to specify indexes of atoms to apply bond distortions to
2. Add Dimer distortion where 2 of the defect nearest neighbours (the ones closer together) are pushed to a distance of 2 A
3. Add early-on detection of distortions that are stuck in high energy basins and rename them to "High_Energy" to avoid continuing their relaxation