Fix copying of TMolecule

[foxtran]

By some reason, GCC 12.2 does not copy some data between TMolecule objects and, therefore, there is some trash in output like (it is xtbopt.xyz):

This patch fixes it. Not sure that I found all places, but at least GFN2 geometry optimizations work well.

[thfroitzheim]

@foxtran does this still fix a problem? If yes, I would merge it

[foxtran]

I would prefer to implement check in LLVM flang firstly to find all problematic places.