How To Use The Amorphous Gray-Scott Simulator


  1. Introduction and Console Description
  2. The Controls
  3. Configuring The Simulator
  4. Setting Initial Conditions Manually
  5. The Status Area
  6. Adjusting The Process Parameters

Introduction and Console Description

Each square drawn in the main display area (the upper left area of the console) represents a processor. Each one simulates a locus (ie. reaction site) in the reaction-diffusion process according to the Gray-Scott model. Click on a processor and a circle will appear denoting the "sphere of influence" of a processor: the region that may be affected in one time step due to diffusion. Diffusion is modeled as an exchange process between each processor and all the other processors within its sphere of influence (its neighbors). (The neighbors are also highlighted with a white border whenever a new processor is clicked on.) The status area in the lower left corner will also display detailed information on that processor.

The color of a processor represents the concentration of u at the locus that it simulates. Clicking the Watch v radiobutton displays the concentration of v instead. The color bar, at the lower right hand corner, indicates the ordering of the colors. The two sliders immediately beneath the color bar are used for manually modifying the state of a processor. The value indicated by each slider is printed below it, and the corresponding color can be read off the color bar since the sliders and the color bar are all on the same scale.

At the top right of the console, are the Time indicator and the Update Rate menu. The unit of time is a step and the value displayed during a process run indicates the number of updates that each processor has had a chance to perform. The value of the update rate selection indicates how often the colors of the processors ought to be updated in the main display area. While stepping manually, the value of the update rate selection is ignored and the main display area is updated during each time step.

The Update Rate selection determines the frequency at which the main display is updated. The units are in steps so higher values imply slower updates. At the default value of 10, processors will update their colors every 10 steps. A change in the update rate while paused will become effective after resumption, however the time at which the first update after resuming occurs is determined by the previous rate.

The message line, just beneath the main display area, most of the time indicates the neighborhood information. It also reports on the applet's progress when new simulators are being constructed, which can be a timely process for large numbers of processors. If the applet appears unresponsive, check this line for clues on its actual status.

The Controls

  • The New Button creates a new simulator.
    Use this button to make the selections for the number of Processors, the Layout, the Topology and the Radius take effect. Constructing simulators with many processors may be slow, please be patient. Check the Message Line for a progress report.

  • The Reset Button reinitializes the simulator.
    Use this button to set the state of each processor according to the Initialize menu choice, and to make any new parameter values take effect.

  • The Start/Stop/Continue Button acts like the Play button on a VCR.
    Once the simulator has been configured and initialized, click on this button to see the evolution of the process. Click on it again to pause the simulator. Click on it once more to resume. If the button shows Start then clicking on it will cause any new parameter changes (for the process, but not the simulator configuration) to become effective. If the button shows Continue or Stop then any parameter changes since the start of the current process will not take effect. The parameters must remain constant throughout the evolution of the process.

  • The Step By Button evolves the simulation by the number of steps selected in the menu immediately to its right. One "step" here means that each processor computes what its state will be at one dt time unit in the future.

  • The Refresh Button forces the simulator to refresh the entire display area.
    Clicking on this button has no effect on the computation of the process. Use it whenever the window manager fails to redraw the applet's window properly, or to see the current state of the simulator in between automatic screen updates.

    Configuring The Simulator

  • The Processors menu selection indicates the approximate number of processors in the simulation. A selection has no effect until New is clicked. The number to the immediate left of the menu is the actual number of processors placed.

  • The Layout menu selection determines how the processors are laid out. Coordinates range from 0 to 1 on each axis. The explanation describes the coordinates assigned to each processor.
  • The Topology menu selection indicates whether opposite edges of the field ought to be considered adjacent. There are four possibilities:
  • The Radius input box allows the radius of the sphere of influence to be changed. The current value is displayed to the immediate left of the box, and it gets updated only when a New simulator is created. See also Modifying Parameters.

  • The Initialize choice determines how the state variables u and v are initialized. The descriptions below describe the state assigned to each processor.

    Setting State Manually

    When the Initialize selection is set to Manual, clicking Reset causes all the processors to be initialized to the u and v values on the sliders. To set the state for an individual processor, double click on the processor's square in the main display area. The The Status Area will display the information for the processor before and after the change. Multiple processors can be more conveniently set by moving the mouse while keeping the mouse button depressed. Each processor visited in this way will behave as if it had been double clicked.

    Notice that the sliders can still be manipulated, allowing arbitrary initial values for u and v to be set independently on each processor, provided the values lie between 0 and 1 (inclusive). Once all the desired changes have been made, clicking on Start evolves the process starting from the current state.

    NB: While in Manual mode, double clicking on a processor will change its state, even if the process currently being evolved was not initialized with Manual mode. To prevent accidental state modification, select a different Initialize method (say Perturbed Square) after the desired state has been setup.

    The Status Area

    The status area displays information about a processor on which a mouse click is made. The first number is the id of the processor, the number in parentheses is the number of neighbors it has. The pair of numbers after the "@" are the processor's coordinates, and the two numbers after the "=" are the u and v concentrations respectively.

    For example, "1610(12)@(0.605, 0.837)=0.602 0.751" indicates that processor number 1610 has 12 neighbors, is located at coordinates (0.605, 0.837) and currently has u=0.602 and v=0.751.

    When a processor's state is modified manually, its new state is also printed in the status area.

    Modifying Parameters

    Each parameter is associated with two numbers on the simulator's console: one represents its current value, and the other is the value it will assume the next time the simulator is Reset. The number immediately to the right of the parameter name indicates its current value. If the simulator is running, then that value will be used throughout the duration of the current process evolution.

    To change the value of the parameter, edit the box to the right of the parameter name to show the desired new value. There is no need to press Enter or click the mouse after making a change to a parameter's box. The next time the simulator is Reset, the parameters will be updated with the values in the boxes, and the new values will be displayed in the spaces between the parameter titles and the edit boxes.

    Editing the Radius box works just like the parameter boxes. However the value in the box does not get assigned to the radius until the New button is pressed.

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