org.simBio.bio.matsuoka_et_al_2004.molecule
Class Diffusion

java.lang.Object
  extended by org.simBio.core.Component
      extended by org.simBio.core.Parameter
          extended by org.simBio.core.Composite
              extended by org.simBio.core.Reactor
                  extended by org.simBio.bio.matsuoka_et_al_2004.molecule.Diffusion
All Implemented Interfaces:
Node

public class Diffusion
extends Reactor

calculation of diffusion equation.

Since:
rc20
Version:
$Log: Diffusion.java,v $ Revision 1.1 2005/11/01 06:32:38 mikaelwing First version of simBio hosted on sourceforge, version 0.3 Revision 1.1 2005/09/12 04:57:10 sarai rearrenge folder structure as a Maven style Revision 1.2 2005/08/04 08:43:05 sarai revise Javadoc to suppress Warnings
2005/02/01 09:50:01 Some comments were updated to make Javadoc.
2004/12/20 09:29:07 Type of the Oxygen is checked instead of using flag
2004/09/29 04:10:25 Created
Author:
SAITO Ryuta
See Also:
XML example explanation (Japanese, WORD doc)

Field Summary
 double constant
          rate constant of diffusion
 Node external
          external concentration
 Node internal
          internal concentration
 
Fields inherited from class org.simBio.core.Parameter
value
 
Constructor Summary
Diffusion()
           
 
Method Summary
protected  void calculate(double t)
          write equations here, and calculate dy over dt.
 
Methods inherited from class org.simBio.core.Composite
accept, getLink, getNode, getNodesIterator, getNodesSize
 
Methods inherited from class org.simBio.core.Parameter
addValue, getValue, getValueString, prepare, setInitializer, setValue, setValueString, setValueToField
 
Methods inherited from class org.simBio.core.Component
addDydt, end, getIndent, getIndentedShortName, getName, getName, getParent, getRoot, getShortName, getUnits, isNamed, isPrefixed, logIndented, quit, setLinks
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface org.simBio.core.Node
addDydt, addValue, getValue, setValue
 

Field Detail

internal

public Node internal
internal concentration


external

public Node external
external concentration


constant

public double constant
rate constant of diffusion

Constructor Detail

Diffusion

public Diffusion()
Method Detail

calculate

protected void calculate(double t)
Description copied from class: Reactor
write equations here, and calculate dy over dt.
計算中に呼び出される。 計算式を記載する。dy/dtをここで計算する。

Specified by:
calculate in class Reactor
Parameters:
t - elapsed time (ms)


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