Q: The simulation windows have lost the ``Plot'' menu. What's gone wrong?
A: For some bizarre reason I don't understand, the second and subsequent simulation windows in the GUI version don't display the ``Plot'' menu. It is, however, there - it's just hidden. To display it, click on the area just to the right of the last menu item (``Actions'') on the menu bar, and the ``Plot'' menu will magically appear. At least I hope so.
Q: I had two simulations running in the gui. The first (older one) was highlighted and in the foreground, and had finished running. The newer simulation was in the background and was still running. When I used the keyboard shortcut (Alt-C) to close the foreground simulation window, the background one was closed instead. Are keyboard shortcuts grabbed by the most recently opened simulation, irrespective of which has the focus? Should I use the menus instead in such situations?
A: Yes. Yes.
Q: The simulation won't run. I get messages saying ``parse error'' or ``Error parsing input''. What should I do?
A: This is an error processing the input. Make sure your
input file has the correct form (follow the example input file).
In particular it is important to use exactly the correct
relational symbols (
, 
and 
) with the appropriate
input file lines. Additionally, there should be a newline after
the last line in the file.
Q: I'm confused by the above.
A: So will the parser be if you get it wrong.
Q: My input appears to be correct and is correctly parsed. But I nevertheless get run errors.
A: It may be that your input is not valid - for example, you may have chosen concentrations (or the cell volume or concentration scale) such that all particle numbers are zero. One way to spot this is to run the program with a low debug value and to examine the output.