This base class handles the boilerplates methods associated to thresholds + * settings, jacobian and error estimation.
+ * @version $Revision$ $Date$ + * + */ public abstract class AbstractEstimator implements Estimator { /** @@ -227,6 +234,20 @@ public abstract class AbstractEstimator implements Estimator { } + /** + * Solve an estimation problem. + * + *The method should set the parameters of the problem to several + * trial values until it reaches convergence. If this method returns + * normally (i.e. without throwing an exception), then the best + * estimate of the parameters can be retrieved from the problem + * itself, through the {@link EstimationProblem#getAllParameters + * EstimationProblem.getAllParameters} method.
+ * + * @param problem estimation problem to solve + * @exception EstimationException if the problem cannot be solved + * + */ public abstract void estimate(EstimationProblem problem) throws EstimationException; diff --git a/src/java/org/apache/commons/math/estimation/EstimatedParameter.java b/src/java/org/apache/commons/math/estimation/EstimatedParameter.java index 05c71ada3..d5a75e353 100644 --- a/src/java/org/apache/commons/math/estimation/EstimatedParameter.java +++ b/src/java/org/apache/commons/math/estimation/EstimatedParameter.java @@ -117,6 +117,7 @@ public class EstimatedParameter */ private boolean bound; + /** Serializable version identifier */ private static final long serialVersionUID = -555440800213416949L; } diff --git a/src/java/org/apache/commons/math/estimation/GaussNewtonEstimator.java b/src/java/org/apache/commons/math/estimation/GaussNewtonEstimator.java index ebe4c3b81..55246dbc9 100644 --- a/src/java/org/apache/commons/math/estimation/GaussNewtonEstimator.java +++ b/src/java/org/apache/commons/math/estimation/GaussNewtonEstimator.java @@ -170,9 +170,13 @@ public class GaussNewtonEstimator extends AbstractEstimator implements Serializa } + /** Threshold for cost steady state detection. */ private double steadyStateThreshold; + + /** Threshold for cost convergence. */ private double convergence; - private static final long serialVersionUID = 5485001826076289109L; + /** Serializable version identifier */ + private static final long serialVersionUID = 5485001826076289109L; } diff --git a/src/java/org/apache/commons/math/estimation/LevenbergMarquardtEstimator.java b/src/java/org/apache/commons/math/estimation/LevenbergMarquardtEstimator.java index 07cccd5e3..4c1702e22 100644 --- a/src/java/org/apache/commons/math/estimation/LevenbergMarquardtEstimator.java +++ b/src/java/org/apache/commons/math/estimation/LevenbergMarquardtEstimator.java @@ -859,6 +859,7 @@ public class LevenbergMarquardtEstimator extends AbstractEstimator implements Se * and the columns of the jacobian. */ private double orthoTolerance; + /** Serializable version identifier */ private static final long serialVersionUID = -5705952631533171019L; } diff --git a/src/java/org/apache/commons/math/estimation/SimpleEstimationProblem.java b/src/java/org/apache/commons/math/estimation/SimpleEstimationProblem.java index f8af69626..f3b37192a 100644 --- a/src/java/org/apache/commons/math/estimation/SimpleEstimationProblem.java +++ b/src/java/org/apache/commons/math/estimation/SimpleEstimationProblem.java @@ -48,10 +48,18 @@ public class SimpleEstimationProblem implements EstimationProblem { measurements = new ArrayList(); } + /** + * Get all the parameters of the problem. + * @return parameters + */ public EstimatedParameter[] getAllParameters() { return (EstimatedParameter[]) parameters.toArray(new EstimatedParameter[parameters.size()]); } + /** + * Get the unbound parameters of the problem. + * @return unbound parameters + */ public EstimatedParameter[] getUnboundParameters() { // filter the unbound parameters @@ -68,10 +76,17 @@ public class SimpleEstimationProblem implements EstimationProblem { } + /** + * Get the measurements of an estimation problem. + * @return measurements + */ public WeightedMeasurement[] getMeasurements() { return (WeightedMeasurement[]) measurements.toArray(new WeightedMeasurement[measurements.size()]); } + /** Add a parameter to the problem. + * @param p parameter to add + */ protected void addParameter(EstimatedParameter p) { parameters.add(p); } diff --git a/src/java/org/apache/commons/math/estimation/WeightedMeasurement.java b/src/java/org/apache/commons/math/estimation/WeightedMeasurement.java index 530570dd1..4ac52b359 100644 --- a/src/java/org/apache/commons/math/estimation/WeightedMeasurement.java +++ b/src/java/org/apache/commons/math/estimation/WeightedMeasurement.java @@ -154,8 +154,13 @@ public abstract class WeightedMeasurement implements Serializable { return ignored; } + /** Measurement weight. */ private final double weight; + + /** Value of the measurements. */ private final double measuredValue; + + /** Ignore measurement indicator. */ private boolean ignored; } diff --git a/src/java/org/apache/commons/math/fraction/FractionConversionException.java b/src/java/org/apache/commons/math/fraction/FractionConversionException.java index 16499b721..25487def1 100644 --- a/src/java/org/apache/commons/math/fraction/FractionConversionException.java +++ b/src/java/org/apache/commons/math/fraction/FractionConversionException.java @@ -19,6 +19,12 @@ package org.apache.commons.math.fraction; import org.apache.commons.math.MaxIterationsExceededException; +/** + * Error thrown when a double value cannot be converted to a fraction + * in the allowed number of iterations. + * + * @version $Revision$ $Date$ + */ public class FractionConversionException extends MaxIterationsExceededException { /** Serializable version identifier. */ diff --git a/src/java/org/apache/commons/math/geometry/CardanEulerSingularityException.java b/src/java/org/apache/commons/math/geometry/CardanEulerSingularityException.java index 729d5e3c9..babbd3ff6 100644 --- a/src/java/org/apache/commons/math/geometry/CardanEulerSingularityException.java +++ b/src/java/org/apache/commons/math/geometry/CardanEulerSingularityException.java @@ -25,7 +25,6 @@ import org.apache.commons.math.MathException; * @version $Revision$ $Date$ */ - public class CardanEulerSingularityException extends MathException { @@ -38,6 +37,7 @@ public class CardanEulerSingularityException super(isCardan ? "Cardan angles singularity" : "Euler angles singularity", new Object[0]); } + /** Serializable version identifier */ private static final long serialVersionUID = -1360952845582206770L; } diff --git a/src/java/org/apache/commons/math/geometry/NotARotationMatrixException.java b/src/java/org/apache/commons/math/geometry/NotARotationMatrixException.java index e0e3201a5..a6a7c37a9 100644 --- a/src/java/org/apache/commons/math/geometry/NotARotationMatrixException.java +++ b/src/java/org/apache/commons/math/geometry/NotARotationMatrixException.java @@ -38,6 +38,7 @@ public class NotARotationMatrixException super(specifier, parts); } + /** Serializable version identifier */ private static final long serialVersionUID = 5647178478658937642L; } diff --git a/src/java/org/apache/commons/math/geometry/Rotation.java b/src/java/org/apache/commons/math/geometry/Rotation.java index 3191e7cff..1800b4af8 100644 --- a/src/java/org/apache/commons/math/geometry/Rotation.java +++ b/src/java/org/apache/commons/math/geometry/Rotation.java @@ -1028,6 +1028,7 @@ public class Rotation implements Serializable { /** Third coordinate of the vectorial part of the quaternion. */ private final double q3; + /** Serializable version identifier */ private static final long serialVersionUID = 5127795878493115119L; } diff --git a/src/java/org/apache/commons/math/geometry/Vector3D.java b/src/java/org/apache/commons/math/geometry/Vector3D.java index 347a80b00..c54975ed3 100644 --- a/src/java/org/apache/commons/math/geometry/Vector3D.java +++ b/src/java/org/apache/commons/math/geometry/Vector3D.java @@ -354,6 +354,7 @@ public class Vector3D /** Height. */ private final double z; + /** Serializable version identifier */ private static final long serialVersionUID = 7318440192750283659L; } diff --git a/src/java/org/apache/commons/math/linear/BigMatrixImpl.java b/src/java/org/apache/commons/math/linear/BigMatrixImpl.java index 8f8c9ff59..c53c9d304 100644 --- a/src/java/org/apache/commons/math/linear/BigMatrixImpl.java +++ b/src/java/org/apache/commons/math/linear/BigMatrixImpl.java @@ -1095,8 +1095,8 @@ public class BigMatrixImpl implements BigMatrix, Serializable { } /** - * - * @see Object#toString() + * Get a string representation for this matrix. + * @return a string representation for this matrix */ public String toString() { StringBuffer res = new StringBuffer(); diff --git a/src/java/org/apache/commons/math/linear/RealMatrixImpl.java b/src/java/org/apache/commons/math/linear/RealMatrixImpl.java index 1594e1749..613df8229 100644 --- a/src/java/org/apache/commons/math/linear/RealMatrixImpl.java +++ b/src/java/org/apache/commons/math/linear/RealMatrixImpl.java @@ -846,8 +846,8 @@ public class RealMatrixImpl implements RealMatrix, Serializable { } /** - * - * @see java.lang.Object#toString() + * Get a string representation for this matrix. + * @return a string representation for this matrix */ public String toString() { StringBuffer res = new StringBuffer(); diff --git a/src/java/org/apache/commons/math/ode/AbstractStepInterpolator.java b/src/java/org/apache/commons/math/ode/AbstractStepInterpolator.java index 12afcf1e6..b55548e9e 100644 --- a/src/java/org/apache/commons/math/ode/AbstractStepInterpolator.java +++ b/src/java/org/apache/commons/math/ode/AbstractStepInterpolator.java @@ -354,9 +354,17 @@ public abstract class AbstractStepInterpolator throws DerivativeException { } + /** Write the instance to an output channel. + * @param out output channel + * @exception IOException if the instance cannot be written + */ public abstract void writeExternal(ObjectOutput out) throws IOException; + /** Read the instance from an input channel. + * @param in input channel + * @exception IOException if the instance cannot be read + */ public abstract void readExternal(ObjectInput in) throws IOException; diff --git a/src/java/org/apache/commons/math/ode/AdaptiveStepsizeIntegrator.java b/src/java/org/apache/commons/math/ode/AdaptiveStepsizeIntegrator.java index 9303b31ea..131886dce 100644 --- a/src/java/org/apache/commons/math/ode/AdaptiveStepsizeIntegrator.java +++ b/src/java/org/apache/commons/math/ode/AdaptiveStepsizeIntegrator.java @@ -324,15 +324,49 @@ public abstract class AdaptiveStepsizeIntegrator } + /** Integrate the differential equations up to the given time. + *This method solves an Initial Value Problem (IVP).
+ *Since this method stores some internal state variables made + * available in its public interface during integration ({@link + * #getCurrentSignedStepsize()}), it is not thread-safe.
+ * @param equations differential equations to integrate + * @param t0 initial time + * @param y0 initial value of the state vector at t0 + * @param t target time for the integration + * (can be set to a value smaller thant0 for backward integration)
+ * @param y placeholder where to put the state vector at each successful
+ * step (and hence at the end of integration), can be the same object as y0
+ * @throws IntegratorException if the integrator cannot perform integration
+ * @throws DerivativeException this exception is propagated to the caller if
+ * the underlying user function triggers one
+ */
public abstract void integrate (FirstOrderDifferentialEquations equations,
double t0, double[] y0,
double t, double[] y)
throws DerivativeException, IntegratorException;
+ /** Get the current value of the step start time ti.
+ * This method can be called during integration (typically by + * the object implementing the {@link FirstOrderDifferentialEquations + * differential equations} problem) if the value of the current step that + * is attempted is needed.
+ *The result is undefined if the method is called outside of + * calls to {@link #integrate}
+ * @return current value of the step start time ti + */ public double getCurrentStepStart() { return stepStart; } + /** Get the current signed value of the integration stepsize. + *This method can be called during integration (typically by + * the object implementing the {@link FirstOrderDifferentialEquations + * differential equations} problem) if the signed value of the current stepsize + * that is tried is needed.
+ *The result is undefined if the method is called outside of + * calls to {@link #integrate}
+ * @return current signed value of the stepsize + */ public double getCurrentSignedStepsize() { return stepSize; } diff --git a/src/java/org/apache/commons/math/ode/ClassicalRungeKuttaIntegrator.java b/src/java/org/apache/commons/math/ode/ClassicalRungeKuttaIntegrator.java index a3a256831..1e8f71f5f 100644 --- a/src/java/org/apache/commons/math/ode/ClassicalRungeKuttaIntegrator.java +++ b/src/java/org/apache/commons/math/ode/ClassicalRungeKuttaIntegrator.java @@ -46,18 +46,22 @@ package org.apache.commons.math.ode; public class ClassicalRungeKuttaIntegrator extends RungeKuttaIntegrator { + /** Integrator method name. */ private static final String methodName = "classical Runge-Kutta"; + /** Time steps Butcher array. */ private static final double[] c = { 1.0 / 2.0, 1.0 / 2.0, 1.0 }; + /** Internal weights Butcher array. */ private static final double[][] a = { { 1.0 / 2.0 }, { 0.0, 1.0 / 2.0 }, { 0.0, 0.0, 1.0 } }; + /** Propagation weights Butcher array. */ private static final double[] b = { 1.0 / 6.0, 1.0 / 3.0, 1.0 / 3.0, 1.0 / 6.0 }; diff --git a/src/java/org/apache/commons/math/ode/ClassicalRungeKuttaStepInterpolator.java b/src/java/org/apache/commons/math/ode/ClassicalRungeKuttaStepInterpolator.java index d3c86dc55..b82616204 100644 --- a/src/java/org/apache/commons/math/ode/ClassicalRungeKuttaStepInterpolator.java +++ b/src/java/org/apache/commons/math/ode/ClassicalRungeKuttaStepInterpolator.java @@ -104,6 +104,7 @@ class ClassicalRungeKuttaStepInterpolator } + /** Serializable version identifier */ private static final long serialVersionUID = -6576285612589783992L; } diff --git a/src/java/org/apache/commons/math/ode/ContinuousOutputModel.java b/src/java/org/apache/commons/math/ode/ContinuousOutputModel.java index 6c30f8595..f956b5572 100644 --- a/src/java/org/apache/commons/math/ode/ContinuousOutputModel.java +++ b/src/java/org/apache/commons/math/ode/ContinuousOutputModel.java @@ -371,6 +371,7 @@ public class ContinuousOutputModel /** Steps table. */ private ArrayList steps; + /** Serializable version identifier */ private static final long serialVersionUID = 2259286184268533249L; } diff --git a/src/java/org/apache/commons/math/ode/DerivativeException.java b/src/java/org/apache/commons/math/ode/DerivativeException.java index cc09bdc46..a0922e8fd 100644 --- a/src/java/org/apache/commons/math/ode/DerivativeException.java +++ b/src/java/org/apache/commons/math/ode/DerivativeException.java @@ -44,6 +44,7 @@ public class DerivativeException super(cause); } + /** Serializable version identifier */ private static final long serialVersionUID = -4100440615830558122L; } diff --git a/src/java/org/apache/commons/math/ode/DormandPrince54Integrator.java b/src/java/org/apache/commons/math/ode/DormandPrince54Integrator.java index d04bc04d6..c89b09824 100644 --- a/src/java/org/apache/commons/math/ode/DormandPrince54Integrator.java +++ b/src/java/org/apache/commons/math/ode/DormandPrince54Integrator.java @@ -46,12 +46,15 @@ package org.apache.commons.math.ode; public class DormandPrince54Integrator extends EmbeddedRungeKuttaIntegrator { + /** Integrator method name. */ private static final String methodName = "Dormand-Prince 5(4)"; + /** Time steps Butcher array. */ private static final double[] staticC = { 1.0/5.0, 3.0/10.0, 4.0/5.0, 8.0/9.0, 1.0, 1.0 }; + /** Internal weights Butcher array. */ private static final double[][] staticA = { {1.0/5.0}, {3.0/40.0, 9.0/40.0}, @@ -61,15 +64,29 @@ public class DormandPrince54Integrator {35.0/384.0, 0.0, 500.0/1113.0, 125.0/192.0, -2187.0/6784.0, 11.0/84.0} }; + /** Propagation weights Butcher array. */ private static final double[] staticB = { 35.0/384.0, 0.0, 500.0/1113.0, 125.0/192.0, -2187.0/6784.0, 11.0/84.0, 0.0 }; + /** Error array, element 1. */ private static final double e1 = 71.0 / 57600.0; + + // element 2 is zero, so it is neither stored nor used + + /** Error array, element 3. */ private static final double e3 = -71.0 / 16695.0; + + /** Error array, element 4. */ private static final double e4 = 71.0 / 1920.0; + + /** Error array, element 5. */ private static final double e5 = -17253.0 / 339200.0; + + /** Error array, element 6. */ private static final double e6 = 22.0 / 525.0; + + /** Error array, element 7. */ private static final double e7 = -1.0 / 40.0; /** Simple constructor. diff --git a/src/java/org/apache/commons/math/ode/DormandPrince54StepInterpolator.java b/src/java/org/apache/commons/math/ode/DormandPrince54StepInterpolator.java index 759e74fd6..2dc6f1ecf 100644 --- a/src/java/org/apache/commons/math/ode/DormandPrince54StepInterpolator.java +++ b/src/java/org/apache/commons/math/ode/DormandPrince54StepInterpolator.java @@ -172,20 +172,44 @@ class DormandPrince54StepInterpolator /** Initialization indicator for the interpolation vectors. */ private boolean vectorsInitialized; - // last row of the Butcher-array internal weights, note that a71 is null + /** Last row of the Butcher-array internal weights, element 0. */ private static final double a70 = 35.0 / 384.0; + + // element 1 is zero, so it is neither stored nor used + + /** Last row of the Butcher-array internal weights, element 2. */ private static final double a72 = 500.0 / 1113.0; + + /** Last row of the Butcher-array internal weights, element 3. */ private static final double a73 = 125.0 / 192.0; + + /** Last row of the Butcher-array internal weights, element 4. */ private static final double a74 = -2187.0 / 6784.0; + + /** Last row of the Butcher-array internal weights, element 5. */ private static final double a75 = 11.0 / 84.0; - // dense output of Shampine (1986), note that d1 is null + /** Shampine (1986) Dense output, element 0. */ private static final double d0 = -12715105075.0 / 11282082432.0; + + // element 1 is zero, so it is neither stored nor used + + /** Shampine (1986) Dense output, element 2. */ private static final double d2 = 87487479700.0 / 32700410799.0; + + /** Shampine (1986) Dense output, element 3. */ private static final double d3 = -10690763975.0 / 1880347072.0; + + /** Shampine (1986) Dense output, element 4. */ private static final double d4 = 701980252875.0 / 199316789632.0; + + /** Shampine (1986) Dense output, element 5. */ private static final double d5 = -1453857185.0 / 822651844.0; + + /** Shampine (1986) Dense output, element 6. */ private static final double d6 = 69997945.0 / 29380423.0; + /** Serializable version identifier */ private static final long serialVersionUID = 4104157279605906956L; + } diff --git a/src/java/org/apache/commons/math/ode/DormandPrince853Integrator.java b/src/java/org/apache/commons/math/ode/DormandPrince853Integrator.java index ee2ab7852..72a1a249c 100644 --- a/src/java/org/apache/commons/math/ode/DormandPrince853Integrator.java +++ b/src/java/org/apache/commons/math/ode/DormandPrince853Integrator.java @@ -54,68 +54,69 @@ package org.apache.commons.math.ode; public class DormandPrince853Integrator extends EmbeddedRungeKuttaIntegrator { + /** Integrator method name. */ private static final String methodName = "Dormand-Prince 8 (5, 3)"; - private static final double sqrt6 = Math.sqrt(6.0); - + /** Time steps Butcher array. */ private static final double[] staticC = { - (12.0 - 2.0 * sqrt6) / 135.0, (6.0 - sqrt6) / 45.0, (6.0 - sqrt6) / 30.0, - (6.0 + sqrt6) / 30.0, 1.0/3.0, 1.0/4.0, 4.0/13.0, 127.0/195.0, 3.0/5.0, + (12.0 - 2.0 * Math.sqrt(6.0)) / 135.0, (6.0 - Math.sqrt(6.0)) / 45.0, (6.0 - Math.sqrt(6.0)) / 30.0, + (6.0 + Math.sqrt(6.0)) / 30.0, 1.0/3.0, 1.0/4.0, 4.0/13.0, 127.0/195.0, 3.0/5.0, 6.0/7.0, 1.0, 1.0 }; + /** Internal weights Butcher array. */ private static final double[][] staticA = { // k2 - {(12.0 - 2.0 * sqrt6) / 135.0}, + {(12.0 - 2.0 * Math.sqrt(6.0)) / 135.0}, // k3 - {(6.0 - sqrt6) / 180.0, (6.0 - sqrt6) / 60.0}, + {(6.0 - Math.sqrt(6.0)) / 180.0, (6.0 - Math.sqrt(6.0)) / 60.0}, // k4 - {(6.0 - sqrt6) / 120.0, 0.0, (6.0 - sqrt6) / 40.0}, + {(6.0 - Math.sqrt(6.0)) / 120.0, 0.0, (6.0 - Math.sqrt(6.0)) / 40.0}, // k5 - {(462.0 + 107.0 * sqrt6) / 3000.0, 0.0, - (-402.0 - 197.0 * sqrt6) / 1000.0, (168.0 + 73.0 * sqrt6) / 375.0}, + {(462.0 + 107.0 * Math.sqrt(6.0)) / 3000.0, 0.0, + (-402.0 - 197.0 * Math.sqrt(6.0)) / 1000.0, (168.0 + 73.0 * Math.sqrt(6.0)) / 375.0}, // k6 - {1.0 / 27.0, 0.0, 0.0, (16.0 + sqrt6) / 108.0, (16.0 - sqrt6) / 108.0}, + {1.0 / 27.0, 0.0, 0.0, (16.0 + Math.sqrt(6.0)) / 108.0, (16.0 - Math.sqrt(6.0)) / 108.0}, // k7 - {19.0 / 512.0, 0.0, 0.0, (118.0 + 23.0 * sqrt6) / 1024.0, - (118.0 - 23.0 * sqrt6) / 1024.0, -9.0 / 512.0}, + {19.0 / 512.0, 0.0, 0.0, (118.0 + 23.0 * Math.sqrt(6.0)) / 1024.0, + (118.0 - 23.0 * Math.sqrt(6.0)) / 1024.0, -9.0 / 512.0}, // k8 - {13772.0 / 371293.0, 0.0, 0.0, (51544.0 + 4784.0 * sqrt6) / 371293.0, - (51544.0 - 4784.0 * sqrt6) / 371293.0, -5688.0 / 371293.0, 3072.0 / 371293.0}, + {13772.0 / 371293.0, 0.0, 0.0, (51544.0 + 4784.0 * Math.sqrt(6.0)) / 371293.0, + (51544.0 - 4784.0 * Math.sqrt(6.0)) / 371293.0, -5688.0 / 371293.0, 3072.0 / 371293.0}, // k9 {58656157643.0 / 93983540625.0, 0.0, 0.0, - (-1324889724104.0 - 318801444819.0 * sqrt6) / 626556937500.0, - (-1324889724104.0 + 318801444819.0 * sqrt6) / 626556937500.0, + (-1324889724104.0 - 318801444819.0 * Math.sqrt(6.0)) / 626556937500.0, + (-1324889724104.0 + 318801444819.0 * Math.sqrt(6.0)) / 626556937500.0, 96044563816.0 / 3480871875.0, 5682451879168.0 / 281950621875.0, -165125654.0 / 3796875.0}, // k10 {8909899.0 / 18653125.0, 0.0, 0.0, - (-4521408.0 - 1137963.0 * sqrt6) / 2937500.0, - (-4521408.0 + 1137963.0 * sqrt6) / 2937500.0, + (-4521408.0 - 1137963.0 * Math.sqrt(6.0)) / 2937500.0, + (-4521408.0 + 1137963.0 * Math.sqrt(6.0)) / 2937500.0, 96663078.0 / 4553125.0, 2107245056.0 / 137915625.0, -4913652016.0 / 147609375.0, -78894270.0 / 3880452869.0}, // k11 {-20401265806.0 / 21769653311.0, 0.0, 0.0, - (354216.0 + 94326.0 * sqrt6) / 112847.0, - (354216.0 - 94326.0 * sqrt6) / 112847.0, + (354216.0 + 94326.0 * Math.sqrt(6.0)) / 112847.0, + (354216.0 - 94326.0 * Math.sqrt(6.0)) / 112847.0, -43306765128.0 / 5313852383.0, -20866708358144.0 / 1126708119789.0, 14886003438020.0 / 654632330667.0, 35290686222309375.0 / 14152473387134411.0, -1477884375.0 / 485066827.0}, // k12 {39815761.0 / 17514443.0, 0.0, 0.0, - (-3457480.0 - 960905.0 * sqrt6) / 551636.0, - (-3457480.0 + 960905.0 * sqrt6) / 551636.0, + (-3457480.0 - 960905.0 * Math.sqrt(6.0)) / 551636.0, + (-3457480.0 + 960905.0 * Math.sqrt(6.0)) / 551636.0, -844554132.0 / 47026969.0, 8444996352.0 / 302158619.0, -2509602342.0 / 877790785.0, -28388795297996250.0 / 3199510091356783.0, 226716250.0 / 18341897.0, 1371316744.0 / 2131383595.0}, @@ -130,6 +131,7 @@ public class DormandPrince853Integrator }; + /** Propagation weights Butcher array. */ private static final double[] staticB = { 104257.0/1920240.0, 0.0, @@ -146,22 +148,57 @@ public class DormandPrince853Integrator 0.0 }; + /** First error weights array, element 1. */ private static final double e1_01 = 116092271.0 / 8848465920.0; + + // elements 2 to 5 are zero, so they are neither stored nor used + + /** First error weights array, element 6. */ private static final double e1_06 = -1871647.0 / 1527680.0; + + /** First error weights array, element 7. */ private static final double e1_07 = -69799717.0 / 140793660.0; + + /** First error weights array, element 8. */ private static final double e1_08 = 1230164450203.0 / 739113984000.0; + + /** First error weights array, element 9. */ private static final double e1_09 = -1980813971228885.0 / 5654156025964544.0; + + /** First error weights array, element 10. */ private static final double e1_10 = 464500805.0 / 1389975552.0; + + /** First error weights array, element 11. */ private static final double e1_11 = 1606764981773.0 / 19613062656000.0; + + /** First error weights array, element 12. */ private static final double e1_12 = -137909.0 / 6168960.0; + + /** Second error weights array, element 1. */ private static final double e2_01 = -364463.0 / 1920240.0; + + // elements 2 to 5 are zero, so they are neither stored nor used + + /** Second error weights array, element 6. */ private static final double e2_06 = 3399327.0 / 763840.0; + + /** Second error weights array, element 7. */ private static final double e2_07 = 66578432.0 / 35198415.0; + + /** Second error weights array, element 8. */ private static final double e2_08 = -1674902723.0 / 288716400.0; + + /** Second error weights array, element 9. */ private static final double e2_09 = -74684743568175.0 / 176692375811392.0; + + /** Second error weights array, element 10. */ private static final double e2_10 = -734375.0 / 4826304.0; + + /** Second error weights array, element 11. */ private static final double e2_11 = 171414593.0 / 851261400.0; + + /** Second error weights array, element 12. */ private static final double e2_12 = 69869.0 / 3084480.0; /** Simple constructor. diff --git a/src/java/org/apache/commons/math/ode/DormandPrince853StepInterpolator.java b/src/java/org/apache/commons/math/ode/DormandPrince853StepInterpolator.java index d0acc8b75..2e5bf36af 100644 --- a/src/java/org/apache/commons/math/ode/DormandPrince853StepInterpolator.java +++ b/src/java/org/apache/commons/math/ode/DormandPrince853StepInterpolator.java @@ -310,62 +310,143 @@ class DormandPrince853StepInterpolator /** Initialization indicator for the interpolation vectors. */ private boolean vectorsInitialized; - // external weights of the integrator, - // note that b_02 through b_05 are null - private static double b_01 = 104257.0 / 1920240.0; - private static double b_06 = 3399327.0 / 763840.0; - private static double b_07 = 66578432.0 / 35198415.0; - private static double b_08 = -1674902723.0 / 288716400.0; - private static double b_09 = 54980371265625.0 / 176692375811392.0; - private static double b_10 = -734375.0 / 4826304.0; - private static double b_11 = 171414593.0 / 851261400.0; - private static double b_12 = 137909.0 / 3084480.0; + /** Propagation weights, element 1. */ + private static final double b_01 = 104257.0 / 1920240.0; - // k14 for interpolation only - private static double c14 = 1.0 / 10.0; + // elements 2 to 5 are zero, so they are neither stored nor used - private static double k14_01 = 13481885573.0 / 240030000000.0 - b_01; - private static double k14_06 = 0.0 - b_06; - private static double k14_07 = 139418837528.0 / 549975234375.0 - b_07; - private static double k14_08 = -11108320068443.0 / 45111937500000.0 - b_08; - private static double k14_09 = -1769651421925959.0 / 14249385146080000.0 - b_09; - private static double k14_10 = 57799439.0 / 377055000.0 - b_10; - private static double k14_11 = 793322643029.0 / 96734250000000.0 - b_11; - private static double k14_12 = 1458939311.0 / 192780000000.0 - b_12; - private static double k14_13 = -4149.0 / 500000.0; + /** Propagation weights, element 6. */ + private static final double b_06 = 3399327.0 / 763840.0; - // k15 for interpolation only - private static double c15 = 1.0 / 5.0; + /** Propagation weights, element 7. */ + private static final double b_07 = 66578432.0 / 35198415.0; - private static double k15_01 = 1595561272731.0 / 50120273500000.0 - b_01; - private static double k15_06 = 975183916491.0 / 34457688031250.0 - b_06; - private static double k15_07 = 38492013932672.0 / 718912673015625.0 - b_07; - private static double k15_08 = -1114881286517557.0 / 20298710767500000.0 - b_08; - private static double k15_09 = 0.0 - b_09; - private static double k15_10 = 0.0 - b_10; - private static double k15_11 = -2538710946863.0 / 23431227861250000.0 - b_11; - private static double k15_12 = 8824659001.0 / 23066716781250.0 - b_12; - private static double k15_13 = -11518334563.0 / 33831184612500.0; - private static double k15_14 = 1912306948.0 / 13532473845.0; + /** Propagation weights, element 8. */ + private static final double b_08 = -1674902723.0 / 288716400.0; - // k16 for interpolation only - private static double c16 = 7.0 / 9.0; + /** Propagation weights, element 9. */ + private static final double b_09 = 54980371265625.0 / 176692375811392.0; - private static double k16_01 = -13613986967.0 / 31741908048.0 - b_01; - private static double k16_06 = -4755612631.0 / 1012344804.0 - b_06; - private static double k16_07 = 42939257944576.0 / 5588559685701.0 - b_07; - private static double k16_08 = 77881972900277.0 / 19140370552944.0 - b_08; - private static double k16_09 = 22719829234375.0 / 63689648654052.0 - b_09; - private static double k16_10 = 0.0 - b_10; - private static double k16_11 = 0.0 - b_11; - private static double k16_12 = 0.0 - b_12; - private static double k16_13 = -1199007803.0 / 857031517296.0; - private static double k16_14 = 157882067000.0 / 53564469831.0; - private static double k16_15 = -290468882375.0 / 31741908048.0; + /** Propagation weights, element 10. */ + private static final double b_10 = -734375.0 / 4826304.0; - // interpolation weights - // (beware that only the non-null values are in the table) - private static double[][] d = { + /** Propagation weights, element 11. */ + private static final double b_11 = 171414593.0 / 851261400.0; + + /** Propagation weights, element 12. */ + private static final double b_12 = 137909.0 / 3084480.0; + + /** Time step for stage 14 (interpolation only). */ + private static final double c14 = 1.0 / 10.0; + + /** Internal weights for stage 14, element 1. */ + private static final double k14_01 = 13481885573.0 / 240030000000.0 - b_01; + + // elements 2 to 5 are zero, so they are neither stored nor used + + /** Internal weights for stage 14, element 6. */ + private static final double k14_06 = 0.0 - b_06; + + /** Internal weights for stage 14, element 7. */ + private static final double k14_07 = 139418837528.0 / 549975234375.0 - b_07; + + /** Internal weights for stage 14, element 8. */ + private static final double k14_08 = -11108320068443.0 / 45111937500000.0 - b_08; + + /** Internal weights for stage 14, element 9. */ + private static final double k14_09 = -1769651421925959.0 / 14249385146080000.0 - b_09; + + /** Internal weights for stage 14, element 10. */ + private static final double k14_10 = 57799439.0 / 377055000.0 - b_10; + + /** Internal weights for stage 14, element 11. */ + private static final double k14_11 = 793322643029.0 / 96734250000000.0 - b_11; + + /** Internal weights for stage 14, element 12. */ + private static final double k14_12 = 1458939311.0 / 192780000000.0 - b_12; + + /** Internal weights for stage 14, element 13. */ + private static final double k14_13 = -4149.0 / 500000.0; + + /** Time step for stage 15 (interpolation only). */ + private static final double c15 = 1.0 / 5.0; + + + /** Internal weights for stage 15, element 1. */ + private static final double k15_01 = 1595561272731.0 / 50120273500000.0 - b_01; + + // elements 2 to 5 are zero, so they are neither stored nor used + + /** Internal weights for stage 15, element 6. */ + private static final double k15_06 = 975183916491.0 / 34457688031250.0 - b_06; + + /** Internal weights for stage 15, element 7. */ + private static final double k15_07 = 38492013932672.0 / 718912673015625.0 - b_07; + + /** Internal weights for stage 15, element 8. */ + private static final double k15_08 = -1114881286517557.0 / 20298710767500000.0 - b_08; + + /** Internal weights for stage 15, element 9. */ + private static final double k15_09 = 0.0 - b_09; + + /** Internal weights for stage 15, element 10. */ + private static final double k15_10 = 0.0 - b_10; + + /** Internal weights for stage 15, element 11. */ + private static final double k15_11 = -2538710946863.0 / 23431227861250000.0 - b_11; + + /** Internal weights for stage 15, element 12. */ + private static final double k15_12 = 8824659001.0 / 23066716781250.0 - b_12; + + /** Internal weights for stage 15, element 13. */ + private static final double k15_13 = -11518334563.0 / 33831184612500.0; + + /** Internal weights for stage 15, element 14. */ + private static final double k15_14 = 1912306948.0 / 13532473845.0; + + /** Time step for stage 16 (interpolation only). */ + private static final double c16 = 7.0 / 9.0; + + + /** Internal weights for stage 16, element 1. */ + private static final double k16_01 = -13613986967.0 / 31741908048.0 - b_01; + + // elements 2 to 5 are zero, so they are neither stored nor used + + /** Internal weights for stage 16, element 6. */ + private static final double k16_06 = -4755612631.0 / 1012344804.0 - b_06; + + /** Internal weights for stage 16, element 7. */ + private static final double k16_07 = 42939257944576.0 / 5588559685701.0 - b_07; + + /** Internal weights for stage 16, element 8. */ + private static final double k16_08 = 77881972900277.0 / 19140370552944.0 - b_08; + + /** Internal weights for stage 16, element 9. */ + private static final double k16_09 = 22719829234375.0 / 63689648654052.0 - b_09; + + /** Internal weights for stage 16, element 10. */ + private static final double k16_10 = 0.0 - b_10; + + /** Internal weights for stage 16, element 11. */ + private static final double k16_11 = 0.0 - b_11; + + /** Internal weights for stage 16, element 12. */ + private static final double k16_12 = 0.0 - b_12; + + /** Internal weights for stage 16, element 13. */ + private static final double k16_13 = -1199007803.0 / 857031517296.0; + + /** Internal weights for stage 16, element 14. */ + private static final double k16_14 = 157882067000.0 / 53564469831.0; + + /** Internal weights for stage 16, element 15. */ + private static final double k16_15 = -290468882375.0 / 31741908048.0; + + /** Interpolation weights. + * (beware that only the non-null values are in the table) + */ + private static final double[][] d = { { -17751989329.0 / 2106076560.0, 4272954039.0 / 7539864640.0, -118476319744.0 / 38604839385.0, 755123450731.0 / 316657731600.0, @@ -397,6 +478,7 @@ class DormandPrince853StepInterpolator }; + /** Serializable version identifier */ private static final long serialVersionUID = 7152276390558450974L; } diff --git a/src/java/org/apache/commons/math/ode/DummyStepHandler.java b/src/java/org/apache/commons/math/ode/DummyStepHandler.java index 703e9f81a..77d606834 100644 --- a/src/java/org/apache/commons/math/ode/DummyStepHandler.java +++ b/src/java/org/apache/commons/math/ode/DummyStepHandler.java @@ -87,6 +87,7 @@ public class DummyStepHandler /** The only instance. */ private static DummyStepHandler instance = new DummyStepHandler(); + /** Serializable version identifier */ private static final long serialVersionUID = 2731635121223090252L; } diff --git a/src/java/org/apache/commons/math/ode/DummyStepInterpolator.java b/src/java/org/apache/commons/math/ode/DummyStepInterpolator.java index c0fd31d99..12083e610 100644 --- a/src/java/org/apache/commons/math/ode/DummyStepInterpolator.java +++ b/src/java/org/apache/commons/math/ode/DummyStepInterpolator.java @@ -92,12 +92,20 @@ public class DummyStepInterpolator System.arraycopy(currentState, 0, interpolatedState, 0, currentState.length); } + /** Write the instance to an output channel. + * @param out output channel + * @exception IOException if the instance cannot be written + */ public void writeExternal(ObjectOutput out) throws IOException { // save the state of the base class writeBaseExternal(out); } + /** Read the instance from an input channel. + * @param in input channel + * @exception IOException if the instance cannot be read + */ public void readExternal(ObjectInput in) throws IOException { @@ -113,6 +121,7 @@ public class DummyStepInterpolator } + /** Serializable version identifier */ private static final long serialVersionUID = 1708010296707839488L; } diff --git a/src/java/org/apache/commons/math/ode/EmbeddedRungeKuttaIntegrator.java b/src/java/org/apache/commons/math/ode/EmbeddedRungeKuttaIntegrator.java index df99da583..c0d0cf3e9 100644 --- a/src/java/org/apache/commons/math/ode/EmbeddedRungeKuttaIntegrator.java +++ b/src/java/org/apache/commons/math/ode/EmbeddedRungeKuttaIntegrator.java @@ -61,7 +61,7 @@ public abstract class EmbeddedRungeKuttaIntegrator * @param fsal indicate that the method is an fsal * @param c time steps from Butcher array (without the first zero) * @param a internal weights from Butcher array (without the first empty row) - * @param b external weights for the high order method from Butcher array + * @param b propagation weights for the high order method from Butcher array * @param prototype prototype of the step interpolator to use * @param minStep minimal step (must be positive even for backward * integration), the last step can be smaller than this @@ -98,7 +98,7 @@ public abstract class EmbeddedRungeKuttaIntegrator * @param fsal indicate that the method is an fsal * @param c time steps from Butcher array (without the first zero) * @param a internal weights from Butcher array (without the first empty row) - * @param b external weights for the high order method from Butcher array + * @param b propagation weights for the high order method from Butcher array * @param prototype prototype of the step interpolator to use * @param minStep minimal step (must be positive even for backward * integration), the last step can be smaller than this @@ -155,6 +155,22 @@ public abstract class EmbeddedRungeKuttaIntegrator this.safety = safety; } + /** Integrate the differential equations up to the given time. + *This method solves an Initial Value Problem (IVP).
+ *Since this method stores some internal state variables made + * available in its public interface during integration ({@link + * #getCurrentSignedStepsize()}), it is not thread-safe.
+ * @param equations differential equations to integrate + * @param t0 initial time + * @param y0 initial value of the state vector at t0 + * @param t target time for the integration + * (can be set to a value smaller thant0 for backward integration)
+ * @param y placeholder where to put the state vector at each successful
+ * step (and hence at the end of integration), can be the same object as y0
+ * @throws IntegratorException if the integrator cannot perform integration
+ * @throws DerivativeException this exception is propagated to the caller if
+ * the underlying user function triggers one
+ */
public void integrate(FirstOrderDifferentialEquations equations,
double t0, double[] y0,
double t, double[] y)
diff --git a/src/java/org/apache/commons/math/ode/EulerIntegrator.java b/src/java/org/apache/commons/math/ode/EulerIntegrator.java
index bb4b417bb..6b84ee30c 100644
--- a/src/java/org/apache/commons/math/ode/EulerIntegrator.java
+++ b/src/java/org/apache/commons/math/ode/EulerIntegrator.java
@@ -49,14 +49,18 @@ package org.apache.commons.math.ode;
public class EulerIntegrator
extends RungeKuttaIntegrator {
+ /** Integrator method name. */
private static final String methodName = "Euler";
+ /** Time steps Butcher array. */
private static final double[] c = {
};
+ /** Internal weights Butcher array. */
private static final double[][] a = {
};
+ /** Propagation weights Butcher array. */
private static final double[] b = {
1.0
};
diff --git a/src/java/org/apache/commons/math/ode/EulerStepInterpolator.java b/src/java/org/apache/commons/math/ode/EulerStepInterpolator.java
index 0949fbceb..994aff23e 100644
--- a/src/java/org/apache/commons/math/ode/EulerStepInterpolator.java
+++ b/src/java/org/apache/commons/math/ode/EulerStepInterpolator.java
@@ -89,6 +89,7 @@ class EulerStepInterpolator
}
+ /** Serializable version identifier */
private static final long serialVersionUID = -7179861704951334960L;
}
diff --git a/src/java/org/apache/commons/math/ode/FirstOrderConverter.java b/src/java/org/apache/commons/math/ode/FirstOrderConverter.java
index cc27c4676..d0c5d0a0c 100644
--- a/src/java/org/apache/commons/math/ode/FirstOrderConverter.java
+++ b/src/java/org/apache/commons/math/ode/FirstOrderConverter.java
@@ -69,10 +69,22 @@ public class FirstOrderConverter
zDDot = new double[dimension];
}
+ /** Get the dimension of the problem.
+ * The dimension of the first order problem is twice the + * dimension of the underlying second order problem.
+ * @return dimension of the problem + */ public int getDimension() { return 2 * dimension; } + /** Get the current time derivative of the state vector. + * @param t current value of the independent time variable + * @param y array containing the current value of the state vector + * @param yDot placeholder array where to put the time derivative of the state vector + * @throws DerivativeException this exception is propagated to the caller if the + * underlying user function triggers one + */ public void computeDerivatives(double t, double[] y, double[] yDot) throws DerivativeException { diff --git a/src/java/org/apache/commons/math/ode/GillIntegrator.java b/src/java/org/apache/commons/math/ode/GillIntegrator.java index a9d2db654..7d55b4704 100644 --- a/src/java/org/apache/commons/math/ode/GillIntegrator.java +++ b/src/java/org/apache/commons/math/ode/GillIntegrator.java @@ -45,22 +45,24 @@ package org.apache.commons.math.ode; public class GillIntegrator extends RungeKuttaIntegrator { + /** Integrator method name. */ private static final String methodName = "Gill"; - private static final double sqrt2 = Math.sqrt(2.0); - + /** Time steps Butcher array. */ private static final double[] c = { 1.0 / 2.0, 1.0 / 2.0, 1.0 }; + /** Internal weights Butcher array. */ private static final double[][] a = { { 1.0 / 2.0 }, - { (sqrt2 - 1.0) / 2.0, (2.0 - sqrt2) / 2.0 }, - { 0.0, -sqrt2 / 2.0, (2.0 + sqrt2) / 2.0 } + { (Math.sqrt(2.0) - 1.0) / 2.0, (2.0 - Math.sqrt(2.0)) / 2.0 }, + { 0.0, -Math.sqrt(2.0) / 2.0, (2.0 + Math.sqrt(2.0)) / 2.0 } }; + /** Propagation weights Butcher array. */ private static final double[] b = { - 1.0 / 6.0, (2.0 - sqrt2) / 6.0, (2.0 + sqrt2) / 6.0, 1.0 / 6.0 + 1.0 / 6.0, (2.0 - Math.sqrt(2.0)) / 6.0, (2.0 + Math.sqrt(2.0)) / 6.0, 1.0 / 6.0 }; /** Simple constructor. diff --git a/src/java/org/apache/commons/math/ode/GillStepInterpolator.java b/src/java/org/apache/commons/math/ode/GillStepInterpolator.java index b6d5b35df..fb681ead9 100644 --- a/src/java/org/apache/commons/math/ode/GillStepInterpolator.java +++ b/src/java/org/apache/commons/math/ode/GillStepInterpolator.java @@ -111,6 +111,7 @@ class GillStepInterpolator /** Second Gill coefficient. */ private static final double tPq = 2 + Math.sqrt(2.0); + /** Serializable version identifier */ private static final long serialVersionUID = -107804074496313322L; } diff --git a/src/java/org/apache/commons/math/ode/GraggBulirschStoerIntegrator.java b/src/java/org/apache/commons/math/ode/GraggBulirschStoerIntegrator.java index 399727266..e195c8a2c 100644 --- a/src/java/org/apache/commons/math/ode/GraggBulirschStoerIntegrator.java +++ b/src/java/org/apache/commons/math/ode/GraggBulirschStoerIntegrator.java @@ -87,6 +87,7 @@ package org.apache.commons.math.ode; public class GraggBulirschStoerIntegrator extends AdaptiveStepsizeIntegrator { + /** Integrator method name. */ private static final String methodName = "Gragg-Bulirsch-Stoer"; /** Simple constructor. @@ -503,6 +504,22 @@ public class GraggBulirschStoerIntegrator } } + /** Integrate the differential equations up to the given time. + *This method solves an Initial Value Problem (IVP).
+ *Since this method stores some internal state variables made + * available in its public interface during integration ({@link + * #getCurrentSignedStepsize()}), it is not thread-safe.
+ * @param equations differential equations to integrate + * @param t0 initial time + * @param y0 initial value of the state vector at t0 + * @param t target time for the integration + * (can be set to a value smaller thant0 for backward integration)
+ * @param y placeholder where to put the state vector at each successful
+ * step (and hence at the end of integration), can be the same object as y0
+ * @throws IntegratorException if the integrator cannot perform integration
+ * @throws DerivativeException this exception is propagated to the caller if
+ * the underlying user function triggers one
+ */
public void integrate(FirstOrderDifferentialEquations equations,
double t0, double[] y0, double t, double[] y)
throws DerivativeException, IntegratorException {
diff --git a/src/java/org/apache/commons/math/ode/GraggBulirschStoerStepInterpolator.java b/src/java/org/apache/commons/math/ode/GraggBulirschStoerStepInterpolator.java
index af794bf3d..85252d6b2 100644
--- a/src/java/org/apache/commons/math/ode/GraggBulirschStoerStepInterpolator.java
+++ b/src/java/org/apache/commons/math/ode/GraggBulirschStoerStepInterpolator.java
@@ -393,6 +393,7 @@ class GraggBulirschStoerStepInterpolator
}
+ /** Serializable version identifier */
private static final long serialVersionUID = 7320613236731409847L;
}
diff --git a/src/java/org/apache/commons/math/ode/HighamHall54Integrator.java b/src/java/org/apache/commons/math/ode/HighamHall54Integrator.java
index 9f7b60b5e..48f8882ea 100644
--- a/src/java/org/apache/commons/math/ode/HighamHall54Integrator.java
+++ b/src/java/org/apache/commons/math/ode/HighamHall54Integrator.java
@@ -34,12 +34,15 @@ package org.apache.commons.math.ode;
public class HighamHall54Integrator
extends EmbeddedRungeKuttaIntegrator {
+ /** Integrator method name. */
private static final String methodName = "Higham-Hall 5(4)";
+ /** Time steps Butcher array. */
private static final double[] staticC = {
2.0/9.0, 1.0/3.0, 1.0/2.0, 3.0/5.0, 1.0, 1.0
};
+ /** Internal weights Butcher array. */
private static final double[][] staticA = {
{2.0/9.0},
{1.0/12.0, 1.0/4.0},
@@ -49,10 +52,12 @@ public class HighamHall54Integrator
{1.0/12.0, 0.0, 27.0/32.0, -4.0/3.0, 125.0/96.0, 5.0/48.0}
};
+ /** Propagation weights Butcher array. */
private static final double[] staticB = {
1.0/12.0, 0.0, 27.0/32.0, -4.0/3.0, 125.0/96.0, 5.0/48.0, 0.0
};
+ /** Error weights Butcher array. */
private static final double[] staticE = {
-1.0/20.0, 0.0, 81.0/160.0, -6.0/5.0, 25.0/32.0, 1.0/16.0, -1.0/10.0
};
diff --git a/src/java/org/apache/commons/math/ode/HighamHall54StepInterpolator.java b/src/java/org/apache/commons/math/ode/HighamHall54StepInterpolator.java
index 571202ffa..5e994990c 100644
--- a/src/java/org/apache/commons/math/ode/HighamHall54StepInterpolator.java
+++ b/src/java/org/apache/commons/math/ode/HighamHall54StepInterpolator.java
@@ -88,6 +88,7 @@ class HighamHall54StepInterpolator
}
+ /** Serializable version identifier */
private static final long serialVersionUID = -3583240427587318654L;
}
diff --git a/src/java/org/apache/commons/math/ode/IntegratorException.java b/src/java/org/apache/commons/math/ode/IntegratorException.java
index 0e4ccb0ad..2e5dab030 100644
--- a/src/java/org/apache/commons/math/ode/IntegratorException.java
+++ b/src/java/org/apache/commons/math/ode/IntegratorException.java
@@ -44,6 +44,7 @@ public class IntegratorException
super(cause);
}
+ /** Serializable version identifier */
private static final long serialVersionUID = -1215318282266670558L;
}
diff --git a/src/java/org/apache/commons/math/ode/MidpointIntegrator.java b/src/java/org/apache/commons/math/ode/MidpointIntegrator.java
index e7aefb48a..cd8cefbe3 100644
--- a/src/java/org/apache/commons/math/ode/MidpointIntegrator.java
+++ b/src/java/org/apache/commons/math/ode/MidpointIntegrator.java
@@ -42,16 +42,20 @@ package org.apache.commons.math.ode;
public class MidpointIntegrator
extends RungeKuttaIntegrator {
+ /** Integrator method name. */
private static final String methodName = "midpoint";
+ /** Time steps Butcher array. */
private static final double[] c = {
1.0 / 2.0
};
+ /** Internal weights Butcher array. */
private static final double[][] a = {
{ 1.0 / 2.0 }
};
+ /** Propagation weights Butcher array. */
private static final double[] b = {
0.0, 1.0
};
diff --git a/src/java/org/apache/commons/math/ode/MidpointStepInterpolator.java b/src/java/org/apache/commons/math/ode/MidpointStepInterpolator.java
index 11ce3be5f..dfe7db4fa 100644
--- a/src/java/org/apache/commons/math/ode/MidpointStepInterpolator.java
+++ b/src/java/org/apache/commons/math/ode/MidpointStepInterpolator.java
@@ -95,6 +95,7 @@ class MidpointStepInterpolator
}
+ /** Serializable version identifier */
private static final long serialVersionUID = -865524111506042509L;
}
diff --git a/src/java/org/apache/commons/math/ode/RungeKuttaIntegrator.java b/src/java/org/apache/commons/math/ode/RungeKuttaIntegrator.java
index 5137facc3..4cede3b8c 100644
--- a/src/java/org/apache/commons/math/ode/RungeKuttaIntegrator.java
+++ b/src/java/org/apache/commons/math/ode/RungeKuttaIntegrator.java
@@ -51,7 +51,7 @@ public abstract class RungeKuttaIntegrator
* step. The default step handler does nothing.
* @param c time steps from Butcher array (without the first zero)
* @param a internal weights from Butcher array (without the first empty row)
- * @param b external weights for the high order method from Butcher array
+ * @param b propagation weights for the high order method from Butcher array
* @param prototype prototype of the step interpolator to use
* @param step integration step
*/
@@ -138,6 +138,22 @@ public abstract class RungeKuttaIntegrator
}
}
+ /** Integrate the differential equations up to the given time.
+ * This method solves an Initial Value Problem (IVP).
+ *Since this method stores some internal state variables made + * available in its public interface during integration ({@link + * #getCurrentSignedStepsize()}), it is not thread-safe.
+ * @param equations differential equations to integrate + * @param t0 initial time + * @param y0 initial value of the state vector at t0 + * @param t target time for the integration + * (can be set to a value smaller thant0 for backward integration)
+ * @param y placeholder where to put the state vector at each successful
+ * step (and hence at the end of integration), can be the same object as y0
+ * @throws IntegratorException if the integrator cannot perform integration
+ * @throws DerivativeException this exception is propagated to the caller if
+ * the underlying user function triggers one
+ */
public void integrate(FirstOrderDifferentialEquations equations,
double t0, double[] y0,
double t, double[] y)
@@ -254,10 +270,28 @@ public abstract class RungeKuttaIntegrator
}
+ /** Get the current value of the step start time ti.
+ * This method can be called during integration (typically by + * the object implementing the {@link FirstOrderDifferentialEquations + * differential equations} problem) if the value of the current step that + * is attempted is needed.
+ *The result is undefined if the method is called outside of + * calls to {@link #integrate}
+ * @return current value of the step start time ti + */ public double getCurrentStepStart() { return stepStart; } + /** Get the current signed value of the integration stepsize. + *This method can be called during integration (typically by + * the object implementing the {@link FirstOrderDifferentialEquations + * differential equations} problem) if the signed value of the current stepsize + * that is tried is needed.
+ *The result is undefined if the method is called outside of + * calls to {@link #integrate}
+ * @return current signed value of the stepsize + */ public double getCurrentSignedStepsize() { return stepSize; } diff --git a/src/java/org/apache/commons/math/ode/ThreeEighthesIntegrator.java b/src/java/org/apache/commons/math/ode/ThreeEighthesIntegrator.java index 3accd9c6b..4eb698fea 100644 --- a/src/java/org/apache/commons/math/ode/ThreeEighthesIntegrator.java +++ b/src/java/org/apache/commons/math/ode/ThreeEighthesIntegrator.java @@ -45,18 +45,22 @@ package org.apache.commons.math.ode; public class ThreeEighthesIntegrator extends RungeKuttaIntegrator { + /** Integrator method name. */ private static final String methodName = "3/8"; + /** Time steps Butcher array. */ private static final double[] c = { 1.0 / 3.0, 2.0 / 3.0, 1.0 }; + /** Internal weights Butcher array. */ private static final double[][] a = { { 1.0 / 3.0 }, { -1.0 / 3.0, 1.0 }, { 1.0, -1.0, 1.0 } }; + /** Propagation weights Butcher array. */ private static final double[] b = { 1.0 / 8.0, 3.0 / 8.0, 3.0 / 8.0, 1.0 / 8.0 }; diff --git a/src/java/org/apache/commons/math/ode/ThreeEighthesStepInterpolator.java b/src/java/org/apache/commons/math/ode/ThreeEighthesStepInterpolator.java index 5570c5938..c3883fd17 100644 --- a/src/java/org/apache/commons/math/ode/ThreeEighthesStepInterpolator.java +++ b/src/java/org/apache/commons/math/ode/ThreeEighthesStepInterpolator.java @@ -105,6 +105,7 @@ class ThreeEighthesStepInterpolator } + /** Serializable version identifier */ private static final long serialVersionUID = -3345024435978721931L; } diff --git a/src/java/org/apache/commons/math/random/UniformRandomGenerator.java b/src/java/org/apache/commons/math/random/UniformRandomGenerator.java index 666439cd0..ec6baf7d2 100644 --- a/src/java/org/apache/commons/math/random/UniformRandomGenerator.java +++ b/src/java/org/apache/commons/math/random/UniformRandomGenerator.java @@ -24,7 +24,7 @@ package org.apache.commons.math.random; * deviation equal to 1. Generated values fall in the range * [-√3, +√3]. * - * @version $Revision:$ $Date$ + * @version $Revision$ $Date$ */ public class UniformRandomGenerator implements NormalizedRandomGenerator { @@ -48,6 +48,7 @@ public class UniformRandomGenerator implements NormalizedRandomGenerator { /** Underlying generator. */ private RandomGenerator generator; + /** Square root of three. */ private static final double SQRT3 = Math.sqrt(3.0); } diff --git a/src/java/org/apache/commons/math/stat/Frequency.java b/src/java/org/apache/commons/math/stat/Frequency.java index 9adfde5eb..ebf81f2a0 100644 --- a/src/java/org/apache/commons/math/stat/Frequency.java +++ b/src/java/org/apache/commons/math/stat/Frequency.java @@ -436,6 +436,8 @@ public class Frequency implements Serializable { * natural order. Copied from Commons Collections ComparableComparator. */ private class NaturalComparator implements Comparator, Serializable { + + /** Serializable version identifier */ private static final long serialVersionUID = -3852193713161395148L; /** diff --git a/src/java/org/apache/commons/math/stat/descriptive/DescriptiveStatistics.java b/src/java/org/apache/commons/math/stat/descriptive/DescriptiveStatistics.java index 7a21e4969..99476d95f 100644 --- a/src/java/org/apache/commons/math/stat/descriptive/DescriptiveStatistics.java +++ b/src/java/org/apache/commons/math/stat/descriptive/DescriptiveStatistics.java @@ -66,16 +66,34 @@ public class DescriptiveStatistics implements StatisticalSummary, Serializable { */ protected ResizableDoubleArray eDA = new ResizableDoubleArray(); - // UnivariateStatistic stats implementations - can be reset by setters + /** Mean statistic implementation - can be reset by setter. */ private UnivariateStatistic meanImpl = new Mean(); + + /** Geometric mean statistic implementation - can be reset by setter. */ private UnivariateStatistic geometricMeanImpl = new GeometricMean(); + + /** Kurtosis statistic implementation - can be reset by setter. */ private UnivariateStatistic kurtosisImpl = new Kurtosis(); + + /** Maximum statistic implementation - can be reset by setter. */ private UnivariateStatistic maxImpl = new Max(); + + /** Minimum statistic implementation - can be reset by setter. */ private UnivariateStatistic minImpl = new Min(); + + /** Percentile statistic implementation - can be reset by setter. */ private UnivariateStatistic percentileImpl = new Percentile(); + + /** Skewness statistic implementation - can be reset by setter. */ private UnivariateStatistic skewnessImpl = new Skewness(); + + /** Variance statistic implementation - can be reset by setter. */ private UnivariateStatistic varianceImpl = new Variance(); + + /** Sum of squares statistic implementation - can be reset by setter. */ private UnivariateStatistic sumsqImpl = new SumOfSquares(); + + /** Sum statistic implementation - can be reset by setter. */ private UnivariateStatistic sumImpl = new Sum(); /** diff --git a/src/java/org/apache/commons/math/stat/descriptive/SummaryStatistics.java b/src/java/org/apache/commons/math/stat/descriptive/SummaryStatistics.java index f655fc0f2..3da536d9a 100644 --- a/src/java/org/apache/commons/math/stat/descriptive/SummaryStatistics.java +++ b/src/java/org/apache/commons/math/stat/descriptive/SummaryStatistics.java @@ -128,14 +128,28 @@ public class SummaryStatistics implements StatisticalSummary, Serializable { /** variance of values that have been added */ protected Variance variance = new Variance(); - // Statistics implementations - can be reset by setters + /** Sum statistic implementation - can be reset by setter. */ private StorelessUnivariateStatistic sumImpl = sum; + + /** Sum of squares statistic implementation - can be reset by setter. */ private StorelessUnivariateStatistic sumsqImpl = sumsq; + + /** Minimum statistic implementation - can be reset by setter. */ private StorelessUnivariateStatistic minImpl = min; + + /** Maximum statistic implementation - can be reset by setter. */ private StorelessUnivariateStatistic maxImpl = max; + + /** Sum of log statistic implementation - can be reset by setter. */ private StorelessUnivariateStatistic sumLogImpl = sumLog; + + /** Geometric mean statistic implementation - can be reset by setter. */ private StorelessUnivariateStatistic geoMeanImpl = geoMean; + + /** Mean statistic implementation - can be reset by setter. */ private StorelessUnivariateStatistic meanImpl = mean; + + /** Variance statistic implementation - can be reset by setter. */ private StorelessUnivariateStatistic varianceImpl = variance; /** diff --git a/src/java/org/apache/commons/math/stat/descriptive/SummaryStatisticsImpl.java b/src/java/org/apache/commons/math/stat/descriptive/SummaryStatisticsImpl.java index 85bc3b759..9d6b3101f 100644 --- a/src/java/org/apache/commons/math/stat/descriptive/SummaryStatisticsImpl.java +++ b/src/java/org/apache/commons/math/stat/descriptive/SummaryStatisticsImpl.java @@ -35,7 +35,8 @@ public class SummaryStatisticsImpl extends SummaryStatistics implements Serializ public SummaryStatisticsImpl() { super(); } - + + /** Resets all statistics and storage. */ public void clear() { super.clear(); } diff --git a/src/java/org/apache/commons/math/util/TransformerMap.java b/src/java/org/apache/commons/math/util/TransformerMap.java index bfc49aa17..c28fee3f3 100644 --- a/src/java/org/apache/commons/math/util/TransformerMap.java +++ b/src/java/org/apache/commons/math/util/TransformerMap.java @@ -132,6 +132,9 @@ public class TransformerMap implements NumberTransformer, Serializable { * Attempts to transform the Object against the map of * NumberTransformers. Otherwise it returns Double.NaN. * + * @param o the Object to be transformed. + * @return the double value of the Object. + * @throws MathException if the Object can not be transformed into a Double. * @see org.apache.commons.math.util.NumberTransformer#transform(java.lang.Object) */ public double transform(Object o) throws MathException {