I am basically making a Java program that will have to run a lot of calculations pretty quickly(each frame, aiming for at least 30 f/s). These will mostly be trigonometric and p
Lots of very intelligent and well-qualified people have put a lot of effort, over many years, into making the Math functions work as quickly and as accurately as possible. So unless you're smarter than all of them, and have years of free time to spend on this, it's very unlikely that you'll be able to do a better job.
Most of them are native too - they're not actually in Java. So writing faster versions of them in Java is going to be a complete no-go. You're probably best off using a mixture of C and Assembly Language when you come to write your own; and you'll need to know all the quirks of whatever hardware you're going to be running this on.
Moreover, the current implementations have been tested over many years, by the fact that millions of people all around the world are using Java in some way. You're not going to have access to the same body of testers, so your functions will automatically be more error-prone than the standard ones. This is unavoidable.
So are you still thinking about writing your own functions?