Getting Started

This section introduces you to Kinetiscope and some essential things you should know to effectively use the program.

After reading this section, you should next familiarize yourself with the features of Kinetiscope's main window, then work through one or more tutorials to gain some initial experience setting up reaction schemes, running simulations and examining simulation results. If you are already familiar with these basics, you may wish to skip to the section on example simulations to see samples of mechanisms to which Kinetiscope can be applied.

About Kinetiscope

The Kinetiscope program package provides an interactive and easy-to-use method to simulate chemical reactions. Its stochastic simulation technique is fast and accurate, and is well-suited for a wide variety of reactions. Kinetiscope can be used to simulate kinetic systems based on three distinct models of reaction schemes:

Single Reactor Models
where all reactants are contained in a single volume (a compartment);
Compartmental Models
where a number of such compartments are connected with transfer paths in a user-defined way to describe materials transfer; and
Three-Dimensional Models
where a filled spatial volume is represented by a contiguous three-dimensional array of compartments; each compartment is interconnected with its neighbors by transfer paths that allow diffusive, gradient-driven materials transport between compartments.

Kinetiscope is completely self-contained, and requires no additional programming. You simply select the type of system, define its properties, and then input the reaction mechanism in conventional chemical notation, the rate constants for each step, and the run conditions. Kinetiscope will calculate concentration versus time curves as well as pressure, volume, and temperature data, and display the results as graphs and tables.

Simulations are not limited to single-phase systems; a wide variety of inhomogeneous systems, for example, thermogravimetric analysis of a solid, or reactions between gases and solids or in a flowing reactor, can be successfully simulated.

A variety of reaction conditions may be simulated with Kinetiscope, including

  • constant, variable and programmed temperatures
  • constant and variable pressures
  • constant and variable volumes
  • electrochemical reactions under constant and programmed voltage conditions
  • reactions controlled by an external stimulus, such as pulses of actinic light or administration of a bolus

Kinetiscope is a full-featured simulator designed to be used as a research and development tool. Through the unique combination of its simulation options, flexibility and ease of use, Kinetiscope brings the full power of kinetic modelling of complex chemical systems to professional scientists and engineers, without requiring a background in numerical analysis. These features also make Kinetiscope an ideal tool for teaching the principles of chemical reaction kinetics to students and trainees.

Kinetiscope's Features

The Kinetiscope package contains the simulator, library files you need to run the program, and a collection of example simulations and ancillary files which illustrate Kinetiscope's capabilities and demonstrate techniques for setting up different kinds of calculations.

Kinetiscope's features include:

Multi-platform support
Kinetiscope is available as versions that operate on Microsoft Windows, Apple MacOS and Linux. The reaction file format is universal, and files can be opened, edited and simulations run on any supported platform.
User interface
The user interface enables you to directly enter data for your simulation, run the calculation, plot the results, and export graphs and tables of simulation results.
Multitasking
Kinetiscope allows you to run lengthy simulations while keeping your computer available for other tasks. You may work with other reaction schemes while a simulation is in progress. On multicore processors, Kinetiscope will start a new simulation on another core if one is available. Multiple Kinetiscope sessions can run simultaneously.
Run-time features
Multiple mechanism files can be held in memory at once, so you can look at previous results or prepare a new reaction scheme while another is being simulated. You may stop the simulation at any time without losing your data and inspect your results. Kinetiscope can also detect reactions in equilibrium and invoke an emulation algorithm to simulate them; this can save substantial computer time.
Data input
Kinetiscope allows you a wide range of input options, including:
  • Mechanism input. Reaction mechanisms are entered in conventional chemical notation. Their size is limited only by the amount of computer memory available. You may cut-and-paste reaction steps, compartments and transfer path within and between schemes to rapidly construct a full model.
  • Kinetic data for steps in the mechanism. Kinetiscope simulates a reaction using probabilities derived from rate laws for each step in the mechanism. Rate constants may be entered in single-valued or Arrhenius form. You can specify the kinetics for cases where the rate laws do not follow the stoichiometry.
  • Reaction conditions. Pressure, volume and temperature can be held constant or be allowed to vary in any physically meaningful combination. You specify the pressure, volume and temperature conditions and initial concentrations of all reaction species. Kinetiscope asks you to input thermochemical and density data when needed.
  • Initial concentrations. Initial species concentrations may be input manually in individual compartments. For three-dimensional reaction schemes, where the initial concentration profile may be complex and may involve hundreds or thousands of compartments, the concentrations may be set automatically using values read from a text file.
  • Units. You select the time, energy, concentration and length units.
  • System geometry. For three-dimensional reaction schemes, you define the numbers of cells in each direction and their dimensions. For compartmental reaction schemes, you interactively create compartments and define how they are connected.
  • Documentation. An integrated notebook lets you add comments and explanatory text to a reaction mechanism. Three-dimensional and compartmental reaction schemes may also be annotated on the scheme diagram.
Data import/export
The simulation data you generate may be exported as images of graphs, and as tabular text suitable for import into other software packages for further analysis or presentation. Results of three-dimensional simulations may be exported to video files that depict the system's state at different times. You may overlay externally stored data directly onto a graph of your simulation results in order to compare them.
On-line help
In addition to the online manual you are now reading, there are many tool tips (text boxes containing brief explanatory text) available throughout the user interface. A tool tip is activated by hovering the mouse cursor over a feature.
This manual provides a quick tour, and then more detailed explanations, of all these features and more.

System Requirements

In order to run the Kinetiscope program, you need:

  • Personal computer and operating system. Kinetiscope is available for the following platforms:
    • Microsoft Windows Vista, Windows 7 and Windows 8/8.1; both 32-bit and 64-bit versions are available.
    • Apple Mac OS X versions 10.6 and above (64-bit only).
    • Kinetiscope has been tested with Linux Mint version 17.1, Ubuntu version 14.04.2, and Fedora Release 21. Both 32-bit and 64-bit versions are available.
  • Memory. On Windows, Kinetiscope requires a minimum of ~30 Mbytes free memory to load. On Macintosh, Kinetiscope requires a minimum of ~20 Mbytes free memory to load. On Linux, Kinetiscope requires a minimum of ~40 Mbytes free memory to load. In all cases, additional memory beyond the minimum is used to load reaction schemes and results.
  • Graphics hardware. Kinetiscope uses OpenGL to display graphical results for three-dimensional systems. You must have a recent driver installed for your video card to view such results. Please see the openGL.org web site (http://www.opengl.org/wiki/Getting_Started) for more information.

Installing and Removing Kinetiscope

For Windows platforms, the Kinetiscope program package is provided as a single executable installer. After downloading the file, start the installer by double-clicking with the mouse, and follow the on-screen instructions. When you have completed the installation, a Kinetiscope icon will appear on your desktop. You may remove Kinetiscope from your computer using the conventional uninstall method from the Windows Control Panel.

For Macintosh platforms, Kinetiscope is provided as an package(.pkg) file. After downloading, double-click the Kinetiscope package file with the mouse to start the installer, and follow the on-screen instructions. When you have completed the installation, a Kinetiscope icon will appear on your Launchpad. To remove Kinetiscope from a Mac OS platform, drag the Kinetiscope folder found within in the Applications Folder to the Trash icon on the Desktop.

For Linux platforms, Kinetiscope is provided as a compressed archive (.tgz) file. To install, uncompress the .tgz file in your home directory or another chosen directory. A subdirectory named ./Kinetiscope is created and the program package is placed there. For example: to install Kinetiscope in a subdirectory named mysubdir, run the following commands from a terminal window:

mkdir ~/mysubdir
cd ~/mysubdir
tar zxvf ~/Kinetiscope-install.tgz

To start the Kinetiscope program after the installation, run the following commands from a terminal window:

cd ~/mysubdir/Kinetiscope
./kinetiscope&

To uninstall Kinetiscope from a Linux platform, delete the ~/mysubdir/Kinetiscope directory you created in the step above:

(Note: This will delete, without prompting, the ~/mysubdir/Kinetiscope directory and all subdirectories and files within it; be sure you are not deleting any files you have created that you wish to save.)

rmdir -rf ~/mysubdir/Kinetiscope

Using the Mouse

Kinetiscope makes extensive use of mouse operations for the manipulation of reaction schemes and simulation results. These operations include:

  • Single-click of the left mouse button. You may select an item such as a reaction step, a compartment or a transfer path for a subsequent operation with a single mouse click; this highlights the selected item.
  • Double-click of the left mouse button. You may carry out a default operation (typically an edit of the selected item) by double-clicking.
  • Single-click of the right mouse button. This will show a context menu with a selection of further operations. Reaction steps, reaction schemes, compartments, transfer paths and windows of simulation results all have context menus.
  • Drag-and-drop of reaction scheme files. You may load an existing reaction scheme file into Kinetiscope by dragging its icon from a folder on the desktop into the Kinetiscope main window.
  • Rubber-band selection using the left mouse button. In three-dimensional and compartmental reaction schemes, you may select one or more compartments or transfer paths by pressing and holding the left mouse button while resizing the rubber-band box that appears to include the desired items.
  • Zooming of X-Y and spectrogram plots using the left mouse button. You can zoom into specific regions of these graphs by pressing and holding the left mouse button while dragging the rubber-band box to contain the area of interest.
  • Zooming using the mouse wheel. With three-dimensional and compartmental reaction schemes, and with three-dimensional plots, you can zoom in or out on the entire scene by spinning the mouse wheel.
  • Freehand rotation using the left mouse button. With three-dimensional plots, you can rotate the plot to view the data from different perspectives.
  • Hovering the mouse pointer. By hovering over a tool button, a tool tip will appear. In compartmental and three-dimensional reaction schemes, you can view a short summary of the contents of a compartment or transfer path by hovering over the item.

Typographic Conventions

The following conventions are used in this manual:

  • Boxed monospace type is used for anything you must type or enter.

  • Boldface is used to refer to text displayed on an application window or dialog.

  • Underlined terms are hyperlinks to other sections of the User's Manual. Click on them to access more information on the topic.

  • Italics are used to introduce new terms, and are hyperlinked to their definitions in the glossary. Click on the term to access the definition.

  • Italic Boldface is used to indicate menu commands. When menu commands are given in full, the name of the command is preceded by the “path” of menu commands used to reach it. For example, if you are told to choose File|Create, click on File on the main menu bar to open the File submenu. Then click on Create from the submenu.

  • Push buttons are denoted using this notation or by icons inserted in the text like this.

  • A sentence like this tells you what the task ahead is:
    1. Numbered steps tell you what actions you should take in sequential order.

      A numbered step may be followed by a paragraph which gives you more information about this step.

  • A sentence like this tells you what the task ahead is:
    • If there is only one step it will be in this format.