Driving a charge pump with a Mesa 5i25 stepgen

May not be the best way but this uses the stepgens
quadrature mode to get a square wave output:

loadrt stepgen step_type=2 ctrl_type=v
addf stepgen.make-pulses base-thread
addf stepgen.capture-position servo-thread
addf stepgen.update-freq servo-thread
setp stepgen.0.enable true
setp stepgen.0.velocity-cmd 4

 (last command sets output frequency to 1 Hz)
lastly you would link the step output to the desired output pin

something like

net charge_pump_out stepgen.0.phase-A  your_output_pin

If the frequency is not important you can also use the charge_pump component
that generates an output frequency of 1/2 the base thread frequency

man charge_pump