Leading Project for Biosimulation > Cell/Biodynamics Simulation > simBio
 
 
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Processing with Conductor

Conductor manages the function element tree, and performs integration calculations.

Processing Order

  1. conductor implements Runnable.

  2. First Visitor is used by Runnable.run(), and NodeList, ReactorList, and AnalyzerList are created.

    In the case of an instance tree like below, 

    external
	cell
		NaChannel
			4sGate
			2sGate
		/NaChannel
		K1Channel
	/cell
/external

    The order of every node is registered in the NodeList

    external
	cell
		NaChannel
			4sGate
			2sGate
		K1Channel

    , the Reactor order is registered in the ReactorList 

    			4sGate
			2sGate
		NaChannel
		K1Channel
	cell
external

    Analyzer order is registered in the AnalyzerList, the same manner as the ReactorList.

  3. Next, NodeList.setLinks() is called.
  4. When start() is called, a flag for calculating is set and integrate() is called.
    1. In integrate, first of all NodeList.prepare is called.
    2. For each time step, analyzers.analyze(double t), Reactors.calculate(double t), Variables.update(double t) are called. (Note: by specifing Variable class in the xml, the calculation sequence can be changed.)
    3. In Variables, the time step which fulfils the dy/y settings is used, and every Variable is updated. The time step is returned to Conductor.
    4. Calculations are only carried out for the time which has been set in duration.
    5. Finally, NodeList.end() is called.
  5. In conductor, when the Thread ends NodeList.quit() is called.