// EntityEden.java
package com.ibm.almaden.smartgrid.apps.eden;
/*
** Licensed Materials - Property of IBM
**
** (C) COPYRIGHT IBM Corp. 2002 All rights reserved
**
** US Government Users Restricted Rights - Use, duplication or
** disclosure restricted by GSA ADP Schedule Contract with IBM Corp.
**
*/
import java.awt.Color;
import org.jdom.Element;
import com.ibm.almaden.smartgrid.EntityAbstract;
import com.ibm.almaden.smartgrid.util.Debug;
// ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
// || Class EntityEden ||
// |||||||||||||||||||
/**
**
** EntityEden is a class of entities used in the Eden model
** of bacterial growth. EntityEden extends EntityAbstract
**
* An entity is any object or OPC characteristic which is capable
** of Propagating, or FLOWING from one OPC to another.
** Characteristics of OPCs which regulate this flow should be
** class implementations of PropertyAbstract. Entities might be
** a fluid, an electron or electron density,
** local stress, bacteria, heat, temperature, etc.
** Properties might be local elastic constants, local hardness,
** local conductivity, thermal conductivity, heat capacity etc.
**
**
* For the Eden model, an EntityEden instance represents
** a type of bacteria of a specified type TYPE_A, TYPE_B
** or TYPE_C. It has a "food" attribute that represents the
** type of bacteria it will eat.
*For this example, A eats B; B eats C and C eats A.
*
* The EntityEden also has an assigned propagation probability.
*
*
** @author ames Kaufman
** @version $Revision: 1.3 $ $Date: 2003/05/22 15:19:32 $
**
*/
// ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
public class EntityEden extends EntityAbstract {
public static final String FOOD_ID = "food";
public static final String PROBABILITY = "prob";
/**
* Indicator if this entity is alive or dead
* This is only used to pass information internally and is not needed
* externally.
* Because it is transient, it will always start out as false therefore
* the default value must be false. This value is also not written to XML
*/
private transient boolean _dead = false;
/**
* propagation probability for this entity.
*
*/
private double _propagationProb;
/**
* The Type of bacteria that this entity will consume.
*/
private int _foodID = 0;
/**
* Types of bacteria are TYPE_A, TYPE_B and TYPE_C
*
* A eats B; B eats C and C eats A
*/
public static final int TYPE_A = 5;
public static final int TYPE_B = 3;
public static final int TYPE_C = 2;
/**
* ENTITY_A is a predefined EntityEden that has an ID of TYPE_A
* and eats TYPE_B and propagates with a probability of 0.4
*/
public static final EntityEden ENTITY_A = \
new EntityEden(TYPE_A,TYPE_B,0.4);
/**
* ENTITY_B is a predefined EntityEden that has an ID of TYPE_B
* and eats TYPE_C and propagates with a probability of 0.4
*/
public static final EntityEden ENTITY_B = \
new EntityEden(TYPE_B,TYPE_C,0.4);
/**
* ENTITY_C is a predefined EntityEden that has
* an ID of TYPE_C
* and eats TYPE_A and propagates with a probability
* of 0.4
*/
public static final EntityEden ENTITY_C = \
new EntityEden(TYPE_C,TYPE_A,0.4);
/**
* public EntityEden()
*
* Construct an EntityEden with default color and no requirements
* This public constructor is required so that the XML support
* can dynamically build from an XML file.
*/
public EntityEden() {
}
/**
* Builds an Eden entity instance which describes a
* bacteria, the type of bacteria that it eats and
* the propagation probability for this bacteria.
*
*
* @param entityID_ The type of bacteria TYPE_A, TYPE_B or TYPE_C
* @param foodID_ Food: The type of bacteria this one eats
* @param double propagationProb_ The propagation probability
*
*/
public EntityEden(int entityID_, int foodID_, double propagationProb_) {
_propagationProb = propagationProb_;
_entityID = entityID_;
_foodID = foodID_;
// define the color based on type
if (_entityID == TYPE_A) {
_rgbColor = Color.red.getRGB();
} else if (_entityID == TYPE_B) {
_rgbColor = Color.green.getRGB();
} else if (_entityID == TYPE_C) {
_rgbColor = Color.blue.getRGB();
} else {
Debug.error("EntityEden:"," Invalid Entity. entityID="+_entityID);
}
}
/**
* getChild() returns a new copy of the entity when the entity
* flows from a neighboring cell.
* If the entity was immutable, we could just return
* a reference to the same EntityEden but because we will
* dynamically modify _isAlive, we have to return a
* copy of the entity.
* If a method is not supplied, then a clone will be
* returned, which is what this method does.
* But this is here to show that the method exists.
*
* @return EntityAbstract EntityEden implementation
*/
public EntityAbstract getChild() {
EntityEden e = null;
try {
e = (EntityEden)this.clone();
} catch (CloneNotSupportedException cnse) {
Debug.error("EntityEden.getChild","Error",cnse);
}
return e;
}
/**
* Returns the _alive boolean value.
* @return boolean
*/
final boolean isAlive() {
return ! _dead;
}
/**
* getPropProb()()
* returns the propagation probability for this instance
* @return double
*/
public double getPropProb() {
return _propagationProb;
}
/**
* Returns the foodID.
* @return int
*/
public int getFoodID() {
return _foodID;
}
/**
* Sets the foodID.
* @param foodID The foodID to set
*/
public void setFoodID(int foodID) {
_foodID = foodID;
}
/**
* Sets _propagationProb.
* @param propProb The propagationProb to set
*/
public final void setPropProb(double propagationProb) {
_propagationProb = propagationProb;
}
/**
* Sets the alive.
* @param alive true if alive, false if died.
*/
final void setAlive(boolean alive) {
_dead = ! alive;
}
/****************************************************************
** getXML() **
*******************/
/**
*
* Generates an XML representation of an entity object.
* It will be appended to the EntityElement by the XMLOPCCollectionWriter
* These elements contain any data unique to a class
* extending EntityAbstract (this class).
*
* The XML support will generate something like the following for
* the EntityAbstract object. Note that the code in this method has
* added "food="3" to the attributes.
*
*
* <entityAbstract Id="5" color="16711680" \
prob="0.4" food="3">
* <class name="class com.ibm.almaden.\
smartgrid.apps.eden.EntityEden" />
* </entityAbstract>
*
*
*
* This element must contain all data unique to a class
* extending entityAbstract. The first thing the getXML() \
method implementation
* should do in any class extending entityAbstract is to call
* the getXmlElement() method from its superclass to get the basic
* xml for an abstract entity.
*
* Uses the libraries defining Element defined in org.jdom
*
* @see com.ibm.almaden.smartgrid.EntityAbstract
*
*
* @return Element Returns the XML representation for an OPC entity
*
*
*****************************************************************
*/
public Element getXML() {
// It must first call the getXMLElement for the entityAbstract
Element entityElement = super.getXmlElement();
// now add the foodID attribute to the XML.
entityElement.setAttribute(PROBABILITY, "" + this._propagationProb);
entityElement.setAttribute(FOOD_ID, "" + this._foodID);
return entityElement;
}// getXML()
/*************************************************************
** initFromXML() **
*******************/
/**
** This generates a new EntityEden instance from
* an XML representation of the entity.
*
* This method initializes an EntityEden object based on the
* XML that was created by the getXML() method.
* Using the following line of XML, the EntityEden instance
* will be recreated including the "foodID value that this class
* defines.
*
*
* <entityAbstract Id="5" color="16711680" prob="0.4" food="3">
* <class name="class com.ibm.almaden.smartgrid.\
apps.eden.EntityEden" />
* </entityAbstract>
*
*
** Generates a new EntityEden instance from an XML element
* The first thing any entity.initFromXML() method must do
* is call super. initCommonSubsetFromXML() to initialize
* those entities characteristic of any class extending
* entityAbstract.
*
* Uses the libraries
* org.jdom.Element;
*
* @see com.ibm.almaden.smartgrid.EntityAbstract
*
* @param entityElement_ the xml representation of an entity object
*
*
*
***********************************************************
*/
public void initFromXML(Element entityElement_) {
super.initCommonSubsetFromXML(entityElement_);
this._propagationProb = getDoubleAttribute(entityElement_, PROBABILITY);
this._foodID = getIntAttribute(entityElement_, FOOD_ID);
}// initFromXMLL()
} // Class entityEden

// PropertyEden.java
package com.ibm.almaden.smartgrid.apps.eden;
/*
** Licensed Materials - Property of IBM
**
** (C) COPYRIGHT IBM Corp. 2002 All rights reserved
**
** US Government Users Restricted Rights - Use, duplication or
** disclosure restricted by GSA ADP Schedule Contract with IBM Corp.
**
*/
import org.jdom.Element;
import com.ibm.almaden.smartgrid.entityAbstract;
import com.ibm.almaden.smartgrid.PropertyAbstract;
// |||||||||||||||||||||||||||||||||||||||||||||||||||||||
// || Class PropertyEden ||
// |||||||||||||||||||
/**
* The Property class defines any properties that may apply to
* the OPC or its entities.
* In the case of the Eden model, the propertyEden class is
* used in the propagation
* of the entityEden objects.
* If the PropertyId matches the entry ID then the
* propagation probability is increased by the probability value.
* Otherwise it is decreased.
* @see PropertyAbstract
* @see entityAbstract
* @see EntityEden
**
** @author James Kaufman
** @version $Revision: 1.3 $ $Date: 2003/05/22 15:19:32 $
**
*/
public class PropertyEden extends PropertyAbstract {
/**
* Probability of propagation adjustment
*/
private double _probability = 0.0;
/**
* empty constructor.
* Required for XML support.
*/
public PropertyEden() {
super.setPropertyID(0);
super.setPropertyColor(255);
this.setProbability(0.0);
}
/**
* constructor
*
* @param propertyID_ The unique Id associated with this property
* @param probability_ The adjustment to the random probability
* used when determining the propagation of the
* EntityEden with the same ID value.
*
*/
public PropertyEden(int propertyID_, double probability_) {
super.setPropertyID(propertyID_);
super.setPropertyColor(255);
this.setProbability(probability_);
}
/**
* Returns the Probability.
* @return double
*/
public final double getProbability() {
return _probability;
}
/**
* Sets the Probability.
* @param probability The Probability to set
*/
public final void setProbability(double probability_) {
_probability = probability_;
}
/******************************************************
** getXML() **
*******************/
/**
* Generates an Element with the basic information required
* to define a property in the Eden model
* The first thing the getXML() method implementation
* should do in any class extending property abstract is to call
* the getXmlElement() method from its superclass to get the basic
* xml for an abstract property.
*
* Uses the libraries
* org.jdom.Document;
* org.jdom.Element;
*
* @see com.ibm.almaden.smartgrid.PropertyAbstract
*
* @return propertyElement the XML representation of
* an abstract property
*
*
*******************************************************
*/
public Element getXML() {
Element propertyElement = super.getXmlElement();
propertyElement.setAttribute(PROBABILITY, "" + this._probability);
return propertyElement;
}// getXML()
/******************************************************
** initFromXML() **
*******************/
/**
** Required method. Generates a new PropertyEden instance from
* an XML representation of the property.
* The first thing any property.initFromXML() method must do
* is call super. initCommonSubsetFromXML() to initialize
* those properties characteristic of any class extending
* propertyAbstract.
*
* Uses the libraries
* org.jdom.Element;
*
* @see com.ibm.almaden.smartgrid.PropertyAbstract
*
* @param propertyElement_ the xml representation of a property object
*
*******************************************************
*/
public void initFromXML(Element propertyElement_) {
super.initCommonSubsetFromXML(propertyElement_);
this._probability = \
getDoubleAttribute(propertyElement_, PROBABILITY);
}// initFromXMLL()
} // Class Property

// VppEdenInitializer3D.java
package com.ibm.almaden.smartgrid.apps.eden;
/*
** Licensed Materials - Property of IBM
**
** (C) COPYRIGHT IBM Corp. 2002 All rights reserved
**
** US Government Users Restricted Rights - Use,
** duplication or disclosure restricted 
** by GSA ADP Schedule Contract with IBM Corp.
**
*/
import java.util.Random;
import java.util.Vector;
import com.ibm.almaden.smartgrid.Constants;
import com.ibm.almaden.smartgrid.EntityAbstract;
import com.ibm.almaden.smartgrid.OPCAbstract;
import com.ibm.almaden.smartgrid.OPCCollection;
import com.ibm.almaden.smartgrid.SmartGrid;
import com.ibm.almaden.smartgrid.VppDataInitializerAbstract;
import com.ibm.almaden.smartgrid.SGSystemConfig;
import com.ibm.almaden.smartgrid.VppInfo;
import com.ibm.almaden.smartgrid.util.ConfigFile;
import com.ibm.almaden.smartgrid.util.Debug;
// ||||||||||||||||||||||||||||||||||||||||||||||||||
// || Class VppEdenInitializer ||
// ||||||||||||||||||||||||||
/**
**
** The VppEdenInitializer is responsible for setting the initial
** state of a Vpp Instances created by the ProblemBuilder.
*
* This class extends VPPDataInitializerAbstract to do any initialization
* that is unique to our problem. In this case, it will add one of each type
* of bacteria to a collection in the first VPP.
* It will check the eden.cfg file for specified settings and if not found
* then it will randomly choose the OPCs to be initialized.
*
**
** @see com.ibm.almaden.smartgrid.pb.ProblemAutoBuilder
** @see com.ibm.almaden.smartgrid.SmartGrid
** @see com.ibm.almaden.smartgrid.OPCCollection
** @author James Kaufman
** @author Toby Lehman
** @version $Revision: 1.3 $ $Date: 2003/05/22 15:19:32 $
*/
// ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
public class VppEdenInitializer extends VppDataInitializerAbstract {
/**
*** Classname for tracing and debugging
**/
public static final String _className = "VppEdenInitializer";
/**
** We need this for various random numbers.
**
** random number generation
**/
public Random _rnd = new Random(Constants.RANDOM_NUMBER_SEED);
/**
* Some sample entity instances.
*
*/
public EntityEden _eA = EntityEden.ENTITY_A;
public EntityEden _eB = EntityEden.ENTITY_B;
public EntityEden _eC = EntityEden.ENTITY_C;
/*
*************************************************************
** VppEdenInitializer **
****************
*/
/**
** Constructor with the Problem configuration information
*
* @param config_ Reference to the configuration information
*
*************************************************************
*/
public VppEdenInitializer(SGSystemConfig config_) {
super(config_);
} // Constructor()
/************************************************************
** initialize **
********************/
/**
*** Add The initial entities.
* This is called for each of the VPPs that are created by the
* Problem Builder.
*
* @param vppInfo_ VppInfo object describing the VPP that is
* being initialized.
*** @param collectionVect_ Vector of OPCCollection objects.
***
********************************
**/
public void initialize(VppInfo vppInfo_, Vector collectionVect_) {
String methodName = _className + ".initialize: ";
// Only initialize the first VPP
if (vppInfo_._vppNumber == 0) {
// check if index to initialize is set in config entry
ConfigFile problemCfg = _config.getProblemConfigFile();
//
// look for setting in eden.cfg file
// Stanza: [problem] Attribute: SetA
// default to -1 if not found.
int setA = problemCfg.getInt("problem","SetA",-1);
int setB = problemCfg.getInt("problem","SetB",-1);
int setC = problemCfg.getInt("problem","SetC",-1);
this.seedVPP(collectionVect_, _eA,setA);
this.seedVPP(collectionVect_, _eB,setB);
this.seedVPP(collectionVect_, _eC,setC);
}
} // initialize
/************************************************************
** seedVPP **
********************/
/**
* Seed the VPP with some initial entities.
*
* This code selects a middle OPCCollections
* (number/2) and adds
* the specified entity to a random OPC in that
* OPCCollection.
*
* In the future we'd like to add some control
* to the random placement of the coordinates.
*
* @param collectionVect_ Vector of OPCCollection
* objects @param e_ Entity object we will add to a
* random OPC in one of the OPCCollections
***
*** @return void
*************************************************************
**/
private void seedVPP(Vector \
collectionVect_, EntityEden e_, int index_) {
String methodName = _className + ".seedVPP: ";
// loop through the collections
int numCollections = collectionVect_.size();
int middle = numCollections / 2;
// find the middle one
OPCCollection OPCCollection = \
(OPCCollection) collectionVect_.elementAt(middle);
int numOPC = OPCCollection._collectionArray.length;
int index = index_;
if (index < 0 || index >= numOPC) {
// use random OPC
index = _rnd.nextInt(numOPC);
}
OPCAbstract OPC = (OPCAbstract) \
OPCCollection._collectionArray[index];
Debug.msg(methodName, " ***** Seeding collection " + \
middle + " at OPC # = " + index + " ********");
super.addOccupants(OPC, e_);
return;
} // seedVPP()
} // end VppEdenInitializer class

// AppUtilsGeneric.java
package com.ibm.almaden.smartgrid;
/*
** Licensed Materials - Property of IBM
**
** (C) COPYRIGHT IBM Corp. 2002 All rights reserved
**
** US Government Users Restricted Rights - Use, duplication or
** disclosure restricted by GSA ADP Schedule Contract with IBM Corp.
**
*/
import java.io.Serializable;
import com.ibm.almaden.smartgrid.util.ConfigFile;
// |||||||||||||||||||||||||||||||||||||||||||||||||||||||
// || Class AppUtilsGeneric ||
// |||||||||||||||||||||||
/**
* This class is provided to hold utility methods and data that is shared
* by all of the OPCs. This particular class is only a placeholder
* and example. An application programmer would write their own
* implementation of AppUtilsAbstract. The OPC methods can
refer to method * and data in this class as a static reference
in OPCAbstract.
*
* For Example
*
* AppUtilsGeneric utils = \
(AppUtilsGeneric)OPCAbstract.getAppUtils();
* long x =utils.example(10,5);
*
* @see AppUtilsAbstract for additional details.
* @author James Kaufman
* @author John Thomas
*
**
**
**/
// ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
public class AppUtilsGeneric
extends AppUtilsAbstract implements Serializable {
static final long serialVersionUID = -5934169214775107543L;
long runtimeValue = 0;
/**********************************************************
** AppUtilsGeneric ** (constructor)
**************/
/**
* Constructor for the implementation of the AppUtilAbstract class
*
* @param sysConfigFile_ Reference to the grid.cfg contents
* @param problemConfigFile_ Reference to the problem.cfg contents
***********************************************************
*/
public AppUtilsGeneric(ConfigFile \
sysConfigFile_,ConfigFile problemConfigFile_) {
super(sysConfigFile_,problemConfigFile_); // \
set the system config File
runtimeValue = problemConfigFile_.getLong \
("Problem","Runtimevalue",0);
}
/**********************************************************
** example **
**************/
/**
* An example of a utility method using a value originally
* obtained from Config File
*
* @param arg1_ argument 1
* @param arg2 argument 2
* @return value
***********************************************************
*/
public final long example(long arg1_, long arg2_) {
return (arg1_+arg2_)*runtimeValue;
}
} // Class AppUtilsGeneric