The Simulation Settings dialog allows the setting of parameters that control the simulation execution for the model in the active canvas:
- Sampling Interval is the basic simulation input parameter that controls the simulation accuracy and performance. The smaller the Sampling Interval, the higher the accuracy.
- Simulation Time tells how long the simulation should last. The ratio Simulation Time/Sampling Interval defines the number of steps to be executed in the simulation.
- Chart Update Time defines how often the Chart Windows should be updated. This parameter has no impact on simulation results
- Log Update Time defines how often the internal simulation log should be updated. This internal simulation log can be saved by Simulation | Save Simulation Log. This parameter has no impact on simulation results. The Log Update Time is ignored if the simulation is played in step mode.
- All the times are specified in Petri net time units (pt).
- For a new model, all the settings are initialized on the base of user preferences – see the Simulation Extra Options in Preferences dialog box. The current settings are preserved in the model file.
- For the Fast Play and Max Speed Play menu commands, the Current Speed option specifies how many times the simulation speed should increase over the speed in the regular Play mode. In reality, the maximum speed is limited by the hardware on which Cell Illustrator runs. For simulations started with the Play command, Current Speed has no effect. In this mode, 1pt should be executed by the program in 1 second. The Current Speed setting is application-wide and it is not preserved in the model file. The range of Current Speed is controlled by the Max Speed parameter in the Simulation settings in Preferences.
- Continuous Weak Firing enables/disables the weak firing option for continuous processes. By default, if this option off, a process cannot fire if there are not enough tokens in a connected input entity, i.e. if the calculated delta value is greater than the available entity value . Such behavior is in agreement with the Petri Net model, but is sometimes difficult to understand for normal biological reactions. If this option is on and weak firing is enabled, the process can fire even if the connected entity value is smaller than the delta calculated for the current step. In such a case the weak firing scale is calculated using the formula:
o scale = availableDeltaValue / calculatedDeltaValue
After this the delta value for all input and output entities connected to the ?gweak firing?h process are multiplied by the scale. The scale value is less than 1.
- Discrete Weak Firing. Enables/disables the weak firing option for discrete processes. By default this options is off.
- Firing Accuracy. The minimum change value for which a process fires. If the calculated delta value is less than the firing accuracy, the delta value is threaten as zero and the process does not fire. This option is useful for the case of entity value converging to a given value in an asymptotic way.
The Restore Defaults button re-initializes the Simulation Settings with the values from the user preference settings. You need to set simulation parameters prior to starting simulation. All controls are disabled when a simulation is running.