Geometric

Improvements and fixes:

- Improved writing of output in "scan" (for the improper dihedral project).
- PDB reader is now included (for purposes of user-defined fragments in TRIC coordinate system).
- Optimizations using Psi4 engine will make use of user-supplied PDB and/or radii.

Update the constraint dictionary format used in the JSON interface

Includes some changes to logging for improved compatibility with QCArchive ecosystem.

Includes clean-up to Molpro engine including `exe` and `exeargs` command line options (Sebastian Lee).

Replaces `numpy.matrix` with `numpy.ndarray` (Lori Burns, LPW).

Various other fixes and improvements.