org.simBio.core
Class VariableList

java.lang.Object
  extended by java.util.AbstractCollection
      extended by java.util.AbstractList
          extended by java.util.ArrayList
              extended by org.simBio.core.VariableList
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, java.lang.Iterable, java.util.Collection, java.util.List, java.util.RandomAccess
Direct Known Subclasses:
EulerList, RungeKuttaList

public abstract class VariableList
extends java.util.ArrayList

include euler engine & dt adjuster

Version:
$Id: VariableList.java,v 1.3 2007/02/02 04:53:32 nsarai Exp $
Author:
Nobuaki Sarai
See Also:
Serialized Form

Field Summary
protected  double minDt
          minimum dt
protected  ReactorList reactors
          list of reactors
 
Fields inherited from class java.util.AbstractList
modCount
 
Constructor Summary
VariableList()
           
 
Method Summary
protected  double adjustDt()
          restrict maximum dy/Y and adjust time step
全てのVariableの最大のdy/yが閾値に合うように、time stepを決定する。 2004/11/12 dtが残り計算時間をオーバーしないように制限。 TODO 時々dt=0となってしまうことがある。
 void logIndented()
          log all Euler's indented name
全てのVariableの名前をログに書き出す。
 void prepare(double min, double max, double dyY, double duration)
          call all Euler's start()
dt controlの閾値を設定し、全てのVariableのstart()を呼び出す。
 void setLinks(ReactorList reactors)
          set reactor list for calculate dydt
abstract  double update(double t)
          solve ordinary differential equations
 
Methods inherited from class java.util.ArrayList
add, add, addAll, addAll, clear, clone, contains, ensureCapacity, get, indexOf, isEmpty, lastIndexOf, remove, remove, removeRange, set, size, toArray, toArray, trimToSize
 
Methods inherited from class java.util.AbstractList
equals, hashCode, iterator, listIterator, listIterator, subList
 
Methods inherited from class java.util.AbstractCollection
containsAll, removeAll, retainAll, toString
 
Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface java.util.List
containsAll, equals, hashCode, iterator, listIterator, listIterator, removeAll, retainAll, subList
 

Field Detail

minDt

protected double minDt
minimum dt


reactors

protected ReactorList reactors
list of reactors

Constructor Detail

VariableList

public VariableList()
Method Detail

update

public abstract double update(double t)
solve ordinary differential equations

Parameters:
t - elapsed time
Returns:
time step

setLinks

public void setLinks(ReactorList reactors)
set reactor list for calculate dydt

Parameters:
reactors -

prepare

public void prepare(double min,
                    double max,
                    double dyY,
                    double duration)
call all Euler's start()
dt controlの閾値を設定し、全てのVariableのstart()を呼び出す。

Parameters:
min - minimum time step
max - maximum time step
dyY - restrict maximum dy/Y and adjust time step
duration - to calculate

adjustDt

protected double adjustDt()
restrict maximum dy/Y and adjust time step
全てのVariableの最大のdy/yが閾値に合うように、time stepを決定する。 2004/11/12 dtが残り計算時間をオーバーしないように制限。 TODO 時々dt=0となってしまうことがある。

Returns:
time step

logIndented

public void logIndented()
log all Euler's indented name
全てのVariableの名前をログに書き出す。



Copyright © 2002-2008 Cell/Biodinamics simulation project. All Rights Reserved.