Code working well on Arduino Uno is not working with Mega 2560
It's not working because code you write is code that will work only on ATmega328. Every ATmega328 chip will run this code without any problem.
If you want that Mega does same task as Uno, then you have to rewrite whole code and use Arduino functions(such as pinMode, digitalRead etc..) or read ATmega2560 datasheet and use ATmega2560 registers. Also Search for ATmega2560 pin layout, you'll need it if you want use registers.