Running a Simulation

To simulate a reaction system with Kinetiscope, you must first construct a reaction scheme, where you enter the reaction mechanism, conditions and species data.

Once you have completed that you are ready to put the Kinetiscope simulator to work.

To start a simulation of a reaction scheme:

  1. Set the parameters that control the simulator's operation.
  2. Start the simulator by clicking
  3. Kinetiscope verifies that the reaction conditions and species data are set to values within required limits.

    If not, you will be shown a message box that describes the issue. If this happens, click OK on the message box, correct the settings, and restart the simulator.

  4. If the reaction scheme file contains results from a previous simulation, Kinetiscope will display a message box to confirm that you want to overwrite those data.

    Click Yes on the message box to proceed. If you select No the simulation is cancelled without overwriting the existing simulation results.

  5. If the previous simulation was interrupted when the user clicked the Interrupt Simulation push button on the simulator window, Kinetiscope will display a message box where you may choose to resume the interrupted simulation or restart it.

    Click Resume on the message box to continue with the previous simulation; this retains the existing simulation results. Click Restart on the message box to discard the previous simulation results and begin a new simulation from time zero. If you select Cancel the simulation is cancelled without overwriting the existing simulation results.

  6. If the previous simulation stopped because it reached the event limit or the elapsed time limit you had specified on the Simulation Settings page, you may resume the simulation after specifying a new limit.

    Kinetiscope will display a message box where you choose to continue the simulation from its last time point or restart it. To continue the simulation, enter a new value for the limit and click Resume. Click Restart on the message box to discard the previous simulation results and begin a new simulation from time zero. If you select Cancel the simulation is cancelled without overwriting the existing simulation results.

  7. Once the simulation has successfully started, the scheme window is minimized and the reaction scheme is locked to prevent editing while the simulation is underway.

    A new simulator window is created on the desktop.

Kinetiscope's simulator is run as a separate process on your computer, under the control of Kinetiscope's main window. While a simulation is running, the main window remains available so you may edit or view simulation results of other reaction schemes loaded in memory.

You may start other simulations before the first has ended; these will run in parallel. If the computer processor and operating system allow, new simulations will be started on another CPU core and will not substantially slow other simulations in progress.

The Simulator Window

This window appears when a simulation is active. Any number of simulations may be started at a time; a new simulator window appears for each instance.

The simulator window displays information about the current status of the calculation, showing its internal time, the number of events that have occurred, how long the simulation has been running, and the number of times the system state has been recorded for later analysis.

Stopping the Simulation

The simulation will terminate when one of these conditions occurs:

  • the total reaction probability has fallen to zero because all reactants have been consumed; or
  • The elapsed time in the simulation exceeds the Maximum Time In Simulation limit entered on the Simulation Settings Page ; or
  • The total number of events exceeds the Maximum Number of Events limit entered on the Simulation Settings Page.

When a reaction simulation completes, the simulator window displays the reason it stopped, the total number of events and the time used for this calculation.

To close the simulator window after a completed simulation:

  • Click OK.

If you do not do this in 5 seconds, the window closes automatically. In either case, Kinetiscope then reads and interprets the raw simulation results and saves the interpreted data to the disk file of the reaction scheme. You return to the main window, where you can now plot the results of this simulation.

You may also terminate the simulation manually in two ways.

Normally you will interrupt a simulation, which preserves any simulation results calculated thus far. When you abort rather than interrupt a simulation, any simulation results accumulated to that point are discarded. Only use this second option in the rare event that the simulator window has become unresponsive.

To interrupt a simulation:

  1. From the desktop, make the simulator window the active window.
  2. Click Interrupt Simulation.

    Kinetiscope stops the current simulation immediately, saving the current state of the system as a final data point.

  3. Click OK.
To abort a simulation:
  1. From Kinetiscope's main window, restore (un-minimize) the scheme window of the problematic simulation you wish to abort.
  2. Close the scheme window by
    • Selecting File | Close from the main menu of the main window
    • or
    • Clicking the push button on the main window's tool bar.
  3. On the message box confirming that you want to abort the simulation Click Yes.

    The simulation is aborted without saving the simulation results.

Next Step

Once the simulation is finished, you are now ready to view the results.