Clock Signal
The clock signal in QCADesigner is calculated
as a hard-saturating cosine as shown below. The clock signal is tied directly
to the tunneling energy in the Hamiltonian.

Clock High/Clock Low
Clock low and high values are the saturation energies for the clock signal.
When the clock is high the cell is unlatched. When it is low the cell
is latched. The defaults seem to work in most cases, however, you may
wish to play with them.
Clock Shift
The clock shift allows you to add a positive or negative offset to the
clock as shown in the above figure.
Clock Amplitude Factor
Clock amplitude factor is multiplied by (Clock High - Clock Low) and
reflects the amplitude of the underlying cosine as shown in the above
figure.
Layer Separation
When simulating multilayer QCA circuits, this determines the physical
separation between the different cell layers in [nm].
Maximum Iterations Per Sample
If the design does not converge in this number of iterations, then the simulation
will move on to the next sample point. For complex designs you may wish
to increase this.
Randomize Simulation Order
When active, the order in which cells are simulated is randomized in
each iteration. I recommend leaving this on.
Animate
When active, the circuit will be animated throughout the simulation.
If you zoom into the cells during the simulation you will notice that
the polarization of the cells change.
References