How can Administrator get alerts in sharepoint 2013 farm, when any kind of changes take place in the Central Administration site, like deleting web application, creating web application,adding any user permission I am not looking for particular web application, but on the central admin site as a whole.
I think you are looking for tools to track changes in your entire SharePoint farm right? To track changes to web applications, sites, service application etc I'd recommend SPDocKit. It does not do messaging as far as I know but you can analyze a lot of SharePoint settings and compare them through time. If you want messaging, look into System Center (scom), it can monitor things like memory, database etc. I don't think you can track things like deleting web applications and creating web applications etc.
There is no out of the box which can give you this functionality.
I believe this not required if you organization follows proper Governance Plan and Information Architecture. i.e no one can go in and add/delete web application as such.
If you still want to track then I would recommend creating and Scheduling PowerShell scripts - You need to keep track of current information and compare it will it daily routine (Ex: Number of web applications currently = 3, and daily compare it will this number etc.)