Updates to the file input/output functions in FAME.
Updates to the file input/output functions in FAME.

The changes were needed due to the movement from dynamic to static arrays,
which itself is beneficial because it leaves more of the memory management to
Fortran.

Added logging code to readInput() function in FAME for easier debugging.

Fixed some bugs in writeOutput() as well.

connie/RMG-Java,jwallen/RMG-Java,keceli/RMG-Java,jwallen/RMG-Java,KEHANG/RMG-Java,enochd/RMG-Java,keceli/RMG-Java,rwest/RMG-Java,nyee/RMG-Java,ReactionMechanismGenerator/RMG-Java,KEHANG/RMG-Java,connie/RMG-Java,rwest/RMG-Java,enochd/RMG-Java,nyee/RMG-Java,faribas/RMG-Java,KEHANG/RMG-Java,jwallen/RMG-Java,connie/RMG-Java,ReactionMechanismGenerator/RMG-Java,ReactionMechanismGenerator/RMG-Java,KEHANG/RMG-Java,enochd/RMG-Java,nyee/RMG-Java,faribas/RMG-Java,keceli/RMG-Java,ReactionMechanismGenerator/RMG-Java,nyee/RMG-Java,ReactionMechanismGenerator/RMG-Java,keceli/RMG-Java,connie/RMG-Java,rwest/RMG-Java,rwest/RMG-Java,rwest/RMG-Java,nyee/RMG-Java,keceli/RMG-Java,faribas/RMG-Java,connie/RMG-Java,nyee/RMG-Java,enochd/RMG-Java,faribas/RMG-Java,jwallen/RMG-Java,KEHANG/RMG-Java,enochd/RMG-Java,jwallen/RMG-Java,jwallen/RMG-Java,KEHANG/RMG-Java,enochd/RMG-Java,keceli/RMG-Java