Hey Mohamed Hafez,
Firstly, I shall congratulate you on making this question - it is rather interesting!
Secondly, you should know that ''atone'' and ''repent'' are both considered to be age-old words, the latter being most archaic. That can be explained since they are fairly used in religious contexts.
1) Atone: ''to atone'' means ''to expiate''. When it is followed by ''for'' in a sentence, it gets the meaning of ''make amends or reparation (for a crime, sin, an offence, an error, etc)''.
E.g.: ''You shall atone a guilt with repentance.''
E.g.: ''Do atone for your sins now, and you shall be redeemed.''
E.g.: ''I atoned for your sins before I started going to church again.''
2) Repent: ''to repent'' means 'to feel regret or self-reproach for (something)''. This word is rather archaic and it is commonly used in the sense of ''cause (one or oneself) to feel remorse / to be contrite about (something)''.
E.g.: ''Shall I repent my words?
E.g.: ''He repented of his act.''
E.g.: "And it repented the Lord that he had made man on the earth" (King James Bible).
Hope that helps!!!