Zynq uses the kernel clock framework.
Include the declaration:
#include <linux/clk.h>
Get a handle on the clock you want, by name:
struct clk *fclk = clk_get_sys("FPGA0", NULL);
long requested_rate = 125000000;
Find the nearest supported frequency:
long actual_rate = clk_round_rate(fclk, requested_rate);
Then set the clock rate:
int status;
if ((status = clk_set_rate(fclk, actual_rate))) {
printk(KERN_INFO "[%s:%d] err\n", __FUNCTION__, __LINE__);
return status;
}