Re: [Repast-interest] Simulation ticks are not equal - How to convert to real time?

[harry m. <hme...@ha...>]

Dear all,

I posted this question a while ago, yet I did not get any response. If you
need more info regarding the code, I can provide it.

I think the issue of converting simulation time ticks to real time may be
critical to many other Repast users as well. If there is some good reads on
this topic, I will appreciate if you could refer me to it. 

Thanks a lot,
Harry.



harry meh wrote:
> 
> Dear Jonathan,
> 
> Thanks for your reply. I have copied a number of scheduled methods here:
> 
> Initially I create the seeded cells in the build method of context
> builder:
> 
> 		for (int i=1; i<=howManyCells; i++){
> 			Cell cell = new Cell(“Cell”,space, grid, network);
> 			cellContext.add(cell);
> 			…
> 			vessel.setLocation(new Vector3d(location));
> 			cell.currentLength = 0.0;
> 			space.moveTo(cell, location);
> 			network.addEdge(prevCell, cell);
> 		}
> 
> Then the following method runs for each new agent, with delay = 0.002
> 
> 	private void scheduleStep(double delay){
> 		ISchedule schedule = RunEnvironment.getInstance().getCurrentSchedule();
> 		double currentTick = schedule.getTickCount();
> 		schedule.schedule(ScheduleParameters.createOneTime(currentTick+delay,
>                          ScheduleParameters.FIRST_PRIORITY),new
> StepAction());
> 	}
> 
> The StepAction is an inner class which executes a method performing cell
> elongation, and also calling back the scheduleStep() method. Elongation
> leads to creating a new cell instead of increasing the cell length, when
> the cell length reaches a threshold value.
> 
> 	private void insideStep(){
> 		scheduleStep(0.5);
> 		elongate(UnitElongation); 
> 	}
> 
> This creates a loop that leads to repeated cell elongation, and creation
> of new cells when maximum length is reached.
> 
> There are also other scheduled steps similar to this.
> 
> Best,
> Harry.
> 
> 
> 
> Jonathan Ozik-2 wrote:
>> 
>> Hi Harry,
>> 
>> It might be helpful to see how you're scheduling the relevant methods. If
>> you can send that along, we might be able to figure out what the issue
>> is.
>> 
>> Jonathan
>> 
>> On Jan 25, 2012, at 4:23 PM, harry meh wrote:
>> 
>>> 
>>> Hello,
>>> 
>>> I am developing an agent-based model using Repast. In this simulation, a
>>> limited number of agents (about 40) are created initially, and then
>>> Scheduled methods are used in this agents to reproduce these agents
>>> during
>>> time.
>>> 
>>> This simulation models a biological system, and you can think of it as
>>> biological cells giving birth to new cells by division. As a result of
>>> this
>>> division, the length of the body of tissue increase, and I measure this
>>> increase as a function of time. A number of initial seeds (the number is
>>> chosen randomly, it can be between 3 to 20) are placed on a scaffold and
>>> I
>>> measure the length of tissue created from each seed at fixed time
>>> points. I
>>> also measure the time when first one of the seeds reach the end of
>>> scaffold.
>>> 
>>> Basically, it is expected that the average time to reach the end of
>>> scaffold
>>> to not depend on how many initial seeds exist, as all seeds are
>>> comprised of
>>> similar agent types. To my surprise, this is not true, and when more
>>> seeds
>>> exist, the speed decrease and more time is required.
>>> 
>>> My question is about the scheduling in Repast. Is it happening like when
>>> we
>>> have more actions scheduled, the time ticks take longer time? Otherwise
>>> why
>>> should it take longer to reach the end of the scaffold when we have more
>>> number of agents (in the same conditions)?
>>> 
>>> And I need to convert the time ticks to real time (e.g. hours). I do
>>> this by
>>> comparing simulation results with available experimental results.
>>> However,
>>> due to this inconsistency, I cannot use one single conversion factor,
>>> rather
>>> the conersion factor depends on the number of initial seeds. How can I
>>> avoid
>>> this?
>>> 
>>> I will really appreciate your help, and I hope I have been clear enough.
>>> 
>>> Thanks,
>>> 
>>> Harry.
>>> 
>>> -- 
>>> 
>> 
> 
> 

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