The system clock affects only the behavior of C-mode cells. D-mode operation occurs independent of the system clock. C-mode uses the system clock to control the serial reading and writing of all C-mode cells' truth tables.
     When the simulator first starts, the system clock is stopped. You can run it in two ways:
Step: By hitting the Step button, you advance the clock a single cycle. Hence the truth table of C-mode cells are shifted a single bit.
Run: By hitting the Run button, the clock is continually ticked, allowing free-running operation of all C-mode cells. The Run button will change to a Stop button. Hitting Stop causes the system clock to return to its stopped state.