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Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/commons-math 

Conflicts:
	src/changes/changes.xml
This commit is contained in:
Thomas Neidhart 2015-06-09 20:43:42 +02:00
parent 96eb80efe1 12ec16006a
commit a55ae85447
12 changed files with 124 additions and 59 deletions
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8
doap_math.rdf
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@ -30,10 +30,10 @@
<shortdesc xml:lang="en">Apache Commons Math</shortdesc>
<description xml:lang="en">The Math project is a library of lightweight, self-contained mathematics and statistics components addressing the most common practical problems not immediately available in the Java programming language or commons-lang.</description>
<repository>
<SVNRepository>
<browse rdf:resource="http://svn.apache.org/viewvc/commons/proper/math/trunk/"/>
<location rdf:resource="http://svn.apache.org/repos/asf/commons/proper/math"/>
</SVNRepository>
<GitRepository>
<browse rdf:resource="https://git-wip-us.apache.org/repos/asf?p=commons-math.git"/>
<location rdf:resource="https://git-wip-us.apache.org/repos/asf/commons-math.git"/>
</GitRepository>
</repository>
<release>
<Version>

3
src/changes/changes.xml
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@ -59,6 +59,9 @@ If the output is not quite correct, check for invisible trailing spaces!
when calling "optimize(...)" with linear constraints whose dimension
does not match the dimension of the objective function.
</action>
<action dev="luc" type="fix" issue="MATH-1226"> <!-- backported to 3.6 -->
Fixed wrong event detection in case of close events pairs.
</action>
<action dev="luc" type="add" >
Reimplemented pow(double, double) in FastMath, for better accuracy in
integral power cases and trying to fix erroneous JIT optimization again.

5
src/main/java/org/apache/commons/math4/ode/AbstractIntegrator.java
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@ -292,9 +292,12 @@ public abstract class AbstractIntegrator implements FirstOrderIntegrator {
* @param yDot placeholder array where to put the time derivative of the state vector
* @exception MaxCountExceededException if the number of functions evaluations is exceeded
* @exception DimensionMismatchException if arrays dimensions do not match equations settings
* @exception NullPointerException if the ODE equations have not been set (i.e. if this method
* is called outside of a call to {@link #integrate(ExpandableStatefulODE, double)} or {@link
* #integrate(FirstOrderDifferentialEquations, double, double[], double, double[])})
*/
public void computeDerivatives(final double t, final double[] y, final double[] yDot)
throws MaxCountExceededException, DimensionMismatchException {
throws MaxCountExceededException, DimensionMismatchException, NullPointerException {
evaluations.incrementCount();
expandable.computeDerivatives(t, y, yDot);
}

13
src/main/java/org/apache/commons/math4/ode/events/EventState.java
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@ -296,7 +296,18 @@ public class EventState {
ta = forward ? ta + convergence : ta - convergence;
ga = f.value(ta);
} while ((g0Positive ^ (ga >= 0)) && (forward ^ (ta >= tb)));
--i;
if (forward ^ (ta >= tb)) {
// we were able to skip this spurious root
--i;
} else {
// we can't avoid this root before the end of the step,
// we have to handle it despite it is close to the former one
// maybe we have two very close roots
pendingEventTime = root;
pendingEvent = true;
return true;
}
} else if (Double.isNaN(previousEventTime) ||
(FastMath.abs(previousEventTime - root) > convergence)) {
pendingEventTime = root;

5
src/main/java/org/apache/commons/math4/util/ResizableDoubleArray.java
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@ -179,7 +179,6 @@ public class ResizableDoubleArray implements DoubleArray, Serializable {
* The input array is copied, not referenced.
* Other properties take default values:
* <ul>
* <li>{@code initialCapacity = 16}</li>
* <li>{@code expansionMode = MULTIPLICATIVE}</li>
* <li>{@code expansionFactor = 2.0}</li>
* <li>{@code contractionCriterion = 2.5}</li>
@ -189,7 +188,9 @@ public class ResizableDoubleArray implements DoubleArray, Serializable {
* @since 2.2
*/
public ResizableDoubleArray(double[] initialArray) {
this(DEFAULT_INITIAL_CAPACITY,
this(initialArray == null || initialArray.length == 0 ?
DEFAULT_INITIAL_CAPACITY :
initialArray.length,
DEFAULT_EXPANSION_FACTOR,
DEFAULT_CONTRACTION_DELTA + DEFAULT_EXPANSION_FACTOR,
DEFAULT_EXPANSION_MODE,

12
src/site/design/differentiation.puml
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@ -24,7 +24,7 @@
skinparam NoteFontColor #691616
skinparam ClassFontSize 11
package org.apache.commons.math4 #ECEBD8
package org.apache.commons.math4 #ECEBD8 {
interface "FieldElement<T>" as FieldElement_T_ {
T add(T a)
@ -37,12 +37,12 @@
Field<T> getField()
}
package analysis #DDEBD8
package analysis #DDEBD8 {
interface UnivariateFunction {
double value(double x)
}
package differentiation #DDDBD8
package differentiation #DDDBD8 {
class DerivativeStructure {
-DerivativeStructure(DSCompiler compiler)
@ -98,8 +98,8 @@
UnivariateDifferentiable <-- UnivariateDifferentiator : creates
UnivariateDifferentiable --> DerivativeStructure : uses
end package
end package
end package
}
}
}
@enduml

16
src/site/design/oneD.puml
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@ -24,7 +24,7 @@
skinparam NoteFontColor #691616
skinparam ClassFontSize 11
package org.apache.commons.math4.geometry #ECEBD8
package org.apache.commons.math4.geometry #ECEBD8 {
interface Space {
+int getDimension()
@ -53,15 +53,15 @@
Space <-- Vector_S_
package partitioning #DDEBD8
package partitioning #DDEBD8 {
interface "Region<S extends Space>" as Region_S_
interface "Hyperplane<S extends Space>" as Hyperplane_S_
interface "SubHyperplane<S extends Space>" as SubHyperplane_S_
end package
}
package euclidean #DDEBD8
package euclidean #DDEBD8 {
package oned #DDDBD8
package oned #DDDBD8 {
class Euclidean1D
class OrientedPoint
@ -72,10 +72,10 @@
Vector_S_ <|.. OrientedPoint
Region_S_ <|.. IntervalSet
end package
}
end package
}
end package
}
@enduml

11
src/site/design/partitioning.puml
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@ -24,9 +24,9 @@
skinparam NoteFontColor #691616
skinparam ClassFontSize 11
package org.apache.commons.math4.geometry #ECEBD8
package org.apache.commons.math4.geometry #ECEBD8 {
package partitioning #DDEBD8
package partitioning #DDEBD8 {
abstract "AbstractSubHyperplane<S extends Space, T extends Space>" as AbstractSubHyperplane_S_T_
note left
@ -81,7 +81,7 @@
a region is a part of the space
it may be empty,
it may cover the whole space,
it may have infinite non-closed boudaries,
it may have infinite non-closed boundaries,
it may be in several disconnected sub-parts,
it may contain holes
end note
@ -112,8 +112,7 @@
Region_S_ --> Side
BSPTree_S_ <-- BSPTreeVisitor_S_ : visits
end package
end package
}
}
@enduml

4
src/site/design/solver.puml
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@ -24,7 +24,7 @@
skinparam NoteFontColor #691616
skinparam ClassFontSize 11
package org.apache.commons.math4.differentiation.solvers #ECEBD8
package org.apache.commons.math4.differentiation.solvers #ECEBD8 {
enum AllowedSolution {
ANY_SIDE
@ -97,6 +97,6 @@ abstract class BaseSecantSolver
AbstractPolynomialSolver <|-- LaguerreSolver
AbstractUnivariateSolver <|-- BisectionSolver
end package
}
@enduml

16
src/site/design/threeD.puml
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@ -24,7 +24,7 @@
skinparam NoteFontColor #691616
skinparam ClassFontSize 11
package org.apache.commons.math4.geometry #ECEBD8
package org.apache.commons.math4.geometry #ECEBD8 {
interface Space {
+int getDimension()
@ -53,15 +53,15 @@
Space <-- Vector_S_
package partitioning #DDEBD8
package partitioning #DDEBD8 {
interface "Region<S extends Space>" as Region_S_
interface "Hyperplane<S extends Space>" as Hyperplane_S_
interface "SubHyperplane<S extends Space>" as SubHyperplane_S_
end package
}
package euclidean #DDEBD8
package euclidean #DDEBD8 {
package threed #DDDBD8
package threed #DDDBD8 {
class Euclidean3D
class Vector3D
@ -77,10 +77,10 @@
SubHyperplane_S_ <|.. SubPlane
Region_S_ <|.. PolyhedronsSet
end package
}
end package
}
end package
}
@enduml

16
src/site/design/twoD.puml
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@ -24,7 +24,7 @@
skinparam NoteFontColor #691616
skinparam ClassFontSize 11
package org.apache.commons.math4.geometry #ECEBD8
package org.apache.commons.math4.geometry #ECEBD8 {
interface Space {
+int getDimension()
@ -53,15 +53,15 @@
Space <-- Vector_S_
package partitioning #DDEBD8
package partitioning #DDEBD8 {
interface "Region<S extends Space>" as Region_S_
interface "Hyperplane<S extends Space>" as Hyperplane_S_
interface "SubHyperplane<S extends Space>" as SubHyperplane_S_
end package
}
package euclidean #DDEBD8
package euclidean #DDEBD8 {
package twod #DDDBD8
package twod #DDDBD8 {
class Euclidean2D
class Vector2D
@ -75,10 +75,10 @@
SubHyperplane_S_ <|.. SubLine
Region_S_ <|.. PolygonsSet
end package
}
end package
}
end package
}
@enduml

74
src/test/java/org/apache/commons/math4/ode/events/EventStateTest.java
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@ -29,6 +29,7 @@ import org.apache.commons.math4.ode.SecondaryEquations;
import org.apache.commons.math4.ode.events.EventHandler;
import org.apache.commons.math4.ode.events.EventState;
import org.apache.commons.math4.ode.nonstiff.DormandPrince853Integrator;
import org.apache.commons.math4.ode.nonstiff.LutherIntegrator;
import org.apache.commons.math4.ode.sampling.AbstractStepInterpolator;
import org.apache.commons.math4.ode.sampling.DummyStepInterpolator;
import org.junit.Assert;
@ -43,21 +44,9 @@ public class EventStateTest {
final double r1 = 90.0;
final double r2 = 135.0;
final double gap = r2 - r1;
EventHandler closeEventsGenerator = new EventHandler() {
public void init(double t0, double[] y0, double t) {
}
public void resetState(double t, double[] y) {
}
public double g(double t, double[] y) {
return (t - r1) * (r2 - t);
}
public Action eventOccurred(double t, double[] y, boolean increasing) {
return Action.CONTINUE;
}
};
final double tolerance = 0.1;
EventState es = new EventState(closeEventsGenerator, 1.5 * gap,
EventState es = new EventState(new CloseEventsGenerator(r1, r2), 1.5 * gap,
tolerance, 100,
new BrentSolver(tolerance));
es.setExpandable(new ExpandableStatefulODE(new FirstOrderDifferentialEquations() {
@ -226,4 +215,63 @@ public class EventStateTest {
}
@Test
public void testEventsCloserThanThreshold()
throws DimensionMismatchException, NumberIsTooSmallException,
MaxCountExceededException, NoBracketingException {
FirstOrderDifferentialEquations equation = new FirstOrderDifferentialEquations() {
public int getDimension() {
return 1;
}
public void computeDerivatives(double t, double[] y, double[] yDot) {
yDot[0] = 1.0;
}
};
LutherIntegrator integrator = new LutherIntegrator(20.0);
CloseEventsGenerator eventsGenerator =
new CloseEventsGenerator(9.0 - 1.0 / 128, 9.0 + 1.0 / 128);
integrator.addEventHandler(eventsGenerator, 1.0, 0.02, 1000);
double[] y = new double[1];
double tEnd = integrator.integrate(equation, 0.0, y, 100.0, y);
Assert.assertEquals( 2, eventsGenerator.getCount());
Assert.assertEquals( 9.0 + 1.0 / 128, tEnd, 1.0 / 32.0);
}
private class CloseEventsGenerator implements EventHandler {
final double r1;
final double r2;
int count;
public CloseEventsGenerator(final double r1, final double r2) {
this.r1 = r1;
this.r2 = r2;
this.count = 0;
}
public void init(double t0, double[] y0, double t) {
}
public void resetState(double t, double[] y) {
}
public double g(double t, double[] y) {
return (t - r1) * (r2 - t);
}
public Action eventOccurred(double t, double[] y, boolean increasing) {
return ++count < 2 ? Action.CONTINUE : Action.STOP;
}
public int getCount() {
return count;
}
}
}