3d space problem

[Laurence Clark]

Hi,

I am currently building a stochastic model of bacterial chemotaxis using
Swarm.  So far I have successfully implemented a 2d space (based on the
Heatbugs example) where the molecules involved can collide and react with
each other, and I now want to scale this up to a 3d model.  Since most of
the reactions take place around the cell membrane, a 50 x 50 x 3 space is
all that's required. I have tried to implement this space with a list of 3
pointers to 50x50 Grid2d objects.  The code compiles successfully, but
core-dumps when run.  Below is 
my modified code for displaying the 3 grids, and attached is a .zip file
containing the entire source code.  Can anyone help?

Best wishes, Laurence Clark

----------------------------------------------------------------------

-buildObjects {
  int inc;
  id <Grid2d> currentSpace;
  id <ZoomRaster> spaceRaster;
  id <Object2dDisplay> enzymeDisplay;

  [super buildObjects];
  
  netModelSwarm = [NetModelSwarm create: self];
  
  // Now create probe objects on the model and ourselves. This gives a
  // simple user interface to let the user change parameters.

  CREATE_ARCHIVED_PROBE_DISPLAY (netModelSwarm);
  CREATE_ARCHIVED_PROBE_DISPLAY (self);
 
  // Instruct the control panel to wait for a button event: we halt here
  // until someone hits a control panel button so the user can get a
  // chance to fill in parameters before the simulation runs

  [controlPanel setStateStopped];

  // OK - the user has specified all the parameters for the simulation.
  // Now we're ready to start.

  // First, let the model swarm build its objects.

  [netModelSwarm buildObjects];

  // Now get down to building our own display objects.

  // First, create a colormap: this is a global resource, the information
  // here is used by lots of different objects.

  colormap = [Colormap create: self];

  // Colour 0 is set to green, to display receptor objects
  [colormap setColor: 0 ToName: "green"];

  // Colour 1 is set to red, to display CheY objects
  [colormap setColor: 1 ToName: "red"];

  // Colour 2 is set to blue, to display CheZ objects
  [colormap setColor: 2 ToName: "blue"];

  // Colour 3 is set to yellow, to display CheR objects
  [colormap setColor: 3 ToName: "yellow"];

  // Colour 4 is set to white, to display CheB objects
  [colormap setColor: 4 ToName: "white"];

  // Colour 5 is set to light blue, to display aspartate objects
  [colormap setColor: 5 ToName: "cyan"];

  // Colour 6 is set to purple, to display aspartate objects
  [colormap setColor: 6 ToName: "magenta"];

  // Next, create a 2d window for display, set its size, zoom factor, title.

  space = [netModelSwarm getSpace];
  spaceX = [[space atOffset:0] getSizeX];
  spaceY = [[space atOffset:0] getSizeY];
  spaceZ = [space getCount];


  spaceRasterList = [List create: [self getZone]];
  enzymeDisplayList = [List create: [self getZone]];

  for (inc=0; inc<spaceZ; inc++) {
    currentSpace = [space atOffset:inc];
    spaceRaster = [ZoomRaster createBegin: self];
    SET_WINDOW_GEOMETRY_RECORD_NAME (spaceRaster);
    spaceRaster = [spaceRaster createEnd];
    [spaceRaster enableDestroyNotification: self
                 notificationMethod: @selector (_spaceRasterDeath_:)];
    [spaceRaster setColormap: colormap];
    [spaceRaster setZoomFactor: 4];
    [spaceRaster setWidth: spaceX Height: spaceY];
    [spaceRaster setWindowTitle: "Cell Space"];
    [spaceRaster pack];                           // draw the window.
    [spaceRasterList addLast:spaceRaster];

    // And also create an Object2dDisplay: this object draws heatbugs on
    // the spaceRaster widget for us, and also receives probes.

    enzymeDisplay = 
      [Object2dDisplay create: self
                       setDisplayWidget: spaceRaster
                       setDiscrete2dToDisplay: currentSpace
                       setDisplayMessage: M(drawSelfOn:)];
    
    [enzymeDisplay setObjectCollection: [netModelSwarm getObjectList]];
    [enzymeDisplayList addLast:enzymeDisplay];

    // Also, tell the space raster to send mouse clicks to the enzymeDisplay
    // this allows the user to right-click on the display to probe the enzymes.

    [spaceRaster setButton: ButtonRight
                 Client: enzymeDisplay
                 Message: M(makeProbeAtX:Y:)];
  }

  return self;
}  

- _update_ {
  int inc;
  for (inc=0; inc<[spaceRasterList getCount]; inc++) {
    if ([spaceRasterList atOffset:inc]) {
      [[enzymeDisplayList atOffset:inc] display];
      [[spaceRasterList atOffset:inc] drawSelf]; }}
  return self; }

chemotaxis.zip
Description: Zip archive