Dear Andrew and Steve,
Thank you very much for your comprehensive explanations.
Everything was same between those two read_data files.You are right that “maybe two or more atoms have the same location”. I made a mistake when writing my own home made code. So that, one of the hydrogen atoms had the same position as oxygen atoms. After modification I tested it and I faced to the same outputs.
Thank you very much for your valuable time and effort.
Have a nice day :))