Push Notification in Swift with personal SQL and PHP code

I create app since 1 year now, but I have one interrogation since the beginning. How work push notification when we use our own server ( mysql database and php code , not using Parse ).
There aren't code on the web, and I want to learn how create my own notification .
For example, I have a simple messaging system. When userA send a message to userB, I want to be notify userB .
Can you explain with details the procedure to follow to create this system.