There are many good books about game/simulation design, although most are going to show their examples in other languages. I recommend you pick one up anyway - the concepts will be highly portable and it definitely looks like you need to do some research before starting this project!
On the other hand, maybe all you need is a hint. Here's one - most simulations use a global loop which increments every object once per pass and then updates the screen with the results. Something like:
my $ticks = 0;
while (1) {
$_->update($ticks) foreach (@objects);
$screen->draw(@objects);
$ticks++;
}
Each object is responsible for updating its state and exposes some kind of standard interface used by $screen to do the output (x, y, color, texture, etc). I don't know why you'd bother with XML and log files, but you could consider outputting them similar to re-drawing the screen.
-sam
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