Use map to speed up PreprocessingAtomTypes::atomTypeFromName

Use map to speed up PreprocessingAtomTypes::atomTypeFromName

Previously, we were doing O(numExistingTypes) string comparisons in
PreprocessingAtomTypes::atomTypeFromName.

This significantly slowed down print_bonded function from toputil.cpp,
and, consequently, the pdb2top.

Here, we add an unordered map to store the mapping from type name to
type number, making the whole search O(log(numExistingTypes)), and
avoiding constantly constructing new std::string's from char*'s.

On my machine, this change reduced run time of Pdb2gmx3Test test from ~8
seconds to ~2 seconds.

Closes #3974