How can I drive a stepper motor with Due?

I have used timers and stepper driver to drive a motor but seems the frequency has nothing to do with turning the pump on!

What's the solution to drive a stepper motor?

Thanks!

I have used timers and stepper driver to drive a motor

With what code? What stepper driver?

but seems the frequency has nothing to do with turning the pump on!

What pump?

There is a sticky at the top of the forum that explains how to put together a good post. I'd suggest that you take the time to read it.