The JLS simulator operates in one of two modes - interactive or batch. The interactive mode is run by the user when the GUI is open and a circuit is visible in the editting window. The batch mode is run via the command line. In both cases the circuit is simulated in the same way. The difference is in how the simulator's execution is managed and viewed.
When the simulator is executed all logic elements in the circuit are first initialized to their initial values. The outputs of most logic elements will be initialized to 0. Not gates will be initialized to 1, registers to the initial values given by the user, and state machines to the specified outputs of the initial state. All wires initially carry 0.
Simulation then begins with all elements that output anything other than 0 sending their values through their outputs, along the wires they are connected to, to the inputs of other elements. Each element then performs its respective function with this new input value, perhaps sending a new value through its output after an element-specific delay (propagation delay).
Simulation continues until one of three things happens: