Instructions for use:

Download the entire HoleSim.zip and unzip it. cd to that directory. Start the simulator w/ "java TriangleRegions"

There are three tool modes. Switch between them using the 'm' key. Current mode is displayed in the upper left
-Fill: Fills an area w/ catoms and holes
-Delete: Create a deletion region that will try to empty the selected area. Drag from the surface->the interior of the object.
-Grow: create a growth region that will try to fill the selected area. Drag from the farthest point away->the surface of the object.

There is also a "clear" mode, but it doesn't do anything right now.

To reset the simulator, press the '0' key. This will delete all catoms, holes ,and regions, and reset the clock to 0

to hide display of the region outlines, press the 's' key.

Note that deletion is currently a tad ugly, so you might want to stick w/ growth (deletion works, I'm just not happy wit hit yet).