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Changed usage of ArrayList in interface to regular List.

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This commit is contained in:
Andreas Dräger 2010-02-18 17:52:39 +00:00
parent e69fdc8696
commit 9687ff1fa9
3 changed files with 49 additions and 51 deletions
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9
src/eva2/tools/math/des/EventDESystem.java
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@ -3,7 +3,7 @@
*/
package eva2.tools.math.des;
import java.util.ArrayList;
import java.util.List;
@ -22,13 +22,14 @@ public interface EventDESystem extends DESystem {
* of the species stored in Y. The new values for the species
* are stored in res. The positions in the array returned by this method
* correspond to the positions in Y/res.
* @param res
*
* @return Returns an array with delays for the change of concentration due to events
*/
public ArrayList<DESAssignment> processEvents(double t, double Y[]);
public List<DESAssignment> processEvents(double t, double Y[], double[] res);
public ArrayList<DESAssignment> processAssignmentRules(double t, double Y[]);
public List<DESAssignment> processAssignmentRules(double t, double Y[]);
public ArrayList<DESAssignment> processAlgebraicRules(double t, double Y[]);
public List<DESAssignment> processAlgebraicRules(double t, double Y[]);
}

54
src/eva2/tools/math/des/RKEventSolver.java
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@ -3,19 +3,19 @@ package eva2.tools.math.des;
import java.io.Serializable;
import java.util.ArrayList;
import eva2.tools.math.Mathematics;
/**
* Title: JAVA-EVA Description: Runge-Kutta Method with Events Copyright: Copyright (c) 2002
* Company: University of T&uuml;bingen, Computer Architecture
* Title: JAVA-EVA Description: Runge-Kutta Method with Events Copyright:
* Copyright (c) 2002 Company: University of T&uuml;bingen, Computer
* Architecture
*
* @author Hannes Planatscher
* @author Andreas Dr&auml;ger
* @author Marcel Kronfeld
* @author Alexander D&ouml;rr
* @version 1.1 Status: works, but numerical inaccurate. Modified to process events, e.g. sudden
* changes in the absolute values of the system
* @version 1.1 Status: works, but numerical inaccurate. Modified to process
* events, e.g. sudden changes in the absolute values of the system
*/
public class RKEventSolver extends AbstractDESSolver implements Serializable {
/**
@ -26,6 +26,7 @@ public class RKEventSolver extends AbstractDESSolver implements Serializable {
*
*/
private static boolean useLinearCalc = true;
/**
*
* @param args
@ -70,7 +71,7 @@ public class RKEventSolver extends AbstractDESSolver implements Serializable {
*/
public RKEventSolver(boolean withLinearCalc) {
useLinearCalc = withLinearCalc;
}
/**
@ -78,7 +79,7 @@ public class RKEventSolver extends AbstractDESSolver implements Serializable {
*/
public RKEventSolver(double stepSize) {
this.stepSize = stepSize;
}
/**
@ -327,8 +328,7 @@ public class RKEventSolver extends AbstractDESSolver implements Serializable {
}
/**
* Processes sudden changes in the system due to events in
* the EDES
* Processes sudden changes in the system due to events in the EDES
*
* @param time
* @param Ytemp
@ -339,21 +339,23 @@ public class RKEventSolver extends AbstractDESSolver implements Serializable {
public double[] processEvents(double time, double[] Ytemp,
EventDESystem EDES, double[] change) {
double[] newYtemp = new double[Ytemp.length];
int index;
int index;
for (DESAssignment event : EDES.processEvents(time, Ytemp)) {
index = event.getIndex();
//newYtemp[index] = event.getValue() - (Ytemp[index]);
// newYtemp[index] = event.getValue() - (Ytemp[index]);
newYtemp[index] = event.getValue() - (Ytemp[index] - change[index]);
System.out.printf("time %s: \tYtemp[%s]_old = %s\tYtemp[%s]_new = %s\t change %s \n",
time,index, Ytemp[index], index, (event.getValue() - (Ytemp[index])),change[index]);
}
System.out
.printf(
"time %s: \tYtemp[%s]_old = %s\tYtemp[%s]_new = %s\t change %s \n",
time, index, Ytemp[index], index,
(event.getValue() - (Ytemp[index])), change[index]);
}
return newYtemp;
}
/**
*
* @param time
@ -361,16 +363,14 @@ public class RKEventSolver extends AbstractDESSolver implements Serializable {
* @param EDES
* @return
*/
public void processRules(double time, double[] Ytemp,
EventDESystem EDES){
public void processRules(double time, double[] Ytemp, EventDESystem EDES) {
int index;
for (DESAssignment event : EDES.processAssignmentRules(time, Ytemp)) {
index = event.getIndex();
Ytemp[index] = event.getValue();
}
}
/**
* When set to <code>TRUE</code>, <code>includeTimes</code> will make the
@ -418,21 +418,17 @@ public class RKEventSolver extends AbstractDESSolver implements Serializable {
else
Ytemp = result[i - 1].clone();
// Ytemp = processEventsVoid(x, Ytemp,EDES);
for (int j = 0; j < inbetweensteps; j++) {
if (useLinearCalc)
rkTerm2(EDES, h, x, Ytemp, change);
else
change = rkTerm(EDES, h, x, Ytemp);
// System.out.println("aft change 0 " + change[0]);
Mathematics.vvAdd(Ytemp, change, Ytemp);
if (this.nonnegative) {
for (int k = 0; k < Ytemp.length; k++) {
@ -443,7 +439,7 @@ public class RKEventSolver extends AbstractDESSolver implements Serializable {
x += h;
// process events
// process events
double[] YtempClone2 = processEvents(x, Ytemp, EDES, change);
Mathematics.vvAdd(Ytemp, YtempClone2, Ytemp);
processRules(x, Ytemp, EDES);
@ -469,7 +465,7 @@ public class RKEventSolver extends AbstractDESSolver implements Serializable {
double[] YtempClone = processEvents(x, Ytemp, EDES, change);
Mathematics.vvAdd(Ytemp, YtempClone, Ytemp);
processRules(x, Ytemp, EDES);
if (includeTimes) {
result[i][0] = timePoints[i];
System.arraycopy(Ytemp, 0, result[i], 1, Ytemp.length);
@ -537,14 +533,14 @@ public class RKEventSolver extends AbstractDESSolver implements Serializable {
return result;
}
@Override
// @Override
public double[][] solveAtTimePoints(DESystem DES, double[] initialvalue,
double[] timepoints) {
// TODO Auto-generated method stub
return null;
}
@Override
// @Override
public double[][] solveAtTimePointsWithInitialConditions(DESystem DES,
double[][] initconditions, double[] timepoints) {
// TODO Auto-generated method stub

37
src/eva2/tools/math/des/RKSolverV2.java
View File

@ -326,24 +326,26 @@ public class RKSolverV2 extends AbstractDESSolver implements Serializable {
double[] res = new double[Ytemp.length];
// Arrays.fill(res, 0);
double[] delays = EDES.processEvents(time, Ytemp, res);
System.out.println("delay " +Arrays.toString(delays));
System.out.println("delay " + Arrays.toString(delays));
for (int j = 0; j < delays.length; j++)
if (!Double.isNaN(delays[j])) {
System.out.printf("time %s :Ytemp[%s]_old = %s\tYtemp[%s]_new = %s\n",
time,j, Ytemp[j], j, (res[j] - Ytemp[j]));
Ytemp[j] = res[j] - Ytemp[j];
} else Ytemp[j] = 0d;
if (!Double.isNaN(delays[j])) {
System.out.printf(
"time %s :Ytemp[%s]_old = %s\tYtemp[%s]_new = %s\n",
time, j, Ytemp[j], j, (res[j] - Ytemp[j]));
Ytemp[j] = res[j] - Ytemp[j];
} else
Ytemp[j] = 0d;
return Ytemp;
}
public static boolean containsNaN(double[] arr){
public static boolean containsNaN(double[] arr) {
for (int i = 0; i < arr.length; i++) {
if (Double.isNaN(arr[i]))
return true;
}
return false;
}
@ -408,19 +410,18 @@ public class RKSolverV2 extends AbstractDESSolver implements Serializable {
Ytemp = result[i - 1].clone();
// process events
//double[] YtempClone = processEvents(x, Ytemp.clone(), EDES);
// double[] YtempClone = processEvents(x, Ytemp.clone(), EDES);
// Ytemp = processEventsVoid(x, Ytemp,EDES);
for (int j = 0; j < inbetweensteps; j++) {
if (useLinearCalc)
rkTerm2(EDES, h, x, Ytemp, change);
else
change = rkTerm(EDES, h, x, Ytemp);
// System.out.println("aft change 0 " + change[0]);
Mathematics.vvAdd(Ytemp, change, Ytemp);
if (this.nonnegative) {
for (int k = 0; k < Ytemp.length; k++) {
@ -431,14 +432,14 @@ public class RKSolverV2 extends AbstractDESSolver implements Serializable {
x += h;
// process events
// process events
double[] YtempClone2 = processEvents(x, Ytemp.clone(), EDES);
Mathematics.vvAdd(Ytemp, YtempClone2, Ytemp);
//processEventsVoid(x, Ytemp,EDES);
// processEventsVoid(x, Ytemp,EDES);
}
// ohne wirkung
//Mathematics.vvAdd(Ytemp, YtempClone, Ytemp);
// Mathematics.vvAdd(Ytemp, YtempClone, Ytemp);
h = timePoints[i] - x;
@ -523,14 +524,14 @@ public class RKSolverV2 extends AbstractDESSolver implements Serializable {
return result;
}
@Override
// @Override
public double[][] solveAtTimePoints(DESystem DES, double[] initialvalue,
double[] timepoints) {
// TODO Auto-generated method stub
return null;
}
@Override
// @Override
public double[][] solveAtTimePointsWithInitialConditions(DESystem DES,
double[][] initconditions, double[] timepoints) {
// TODO Auto-generated method stub