support pyGSM to QChem for QMMM system

[shihchengli]

The original version will take into account the geometry of QM and MM regions to generate internal coordinates, but in fact, the MM area will not be moved, so there is no need to generate internal coordinates related to the MM region. I made a small modification here to provide another approach to support the QMMM system. The concept is only generating the internal coordinates about the QM region.

The user needs to support three files, MM_region.txt, link.txt, and frozen.txt.

• Inside MM_region.txt, it includes the geometry information for every MM region atom, following format.
• Inside link.txt, it should have <Bond 1> <Bond 2> <Bond 3> <Bond 4> information for every atom.
• Inside frozen.txt, it includes the index of hydrogen caps. (index starting from 0)

Besides, the starting geometry for GSM should be a cluster model that includes the geometry of the QM region and hydrogen caps for an internal coordinate generation purpose.