@Test
public void testVariableSteps()
throws DimensionMismatchException, NumberIsTooSmallException, MaxCountExceededException,
NoBracketingException {
final TestProblem3 pb = new TestProblem3(0.9);
double minStep = 0;
double maxStep = pb.getFinalTime() - pb.getInitialTime();
double scalAbsoluteTolerance = 1.0e-8;
double scalRelativeTolerance = scalAbsoluteTolerance;
FirstOrderIntegrator integ =
new DormandPrince853Integrator(
minStep, maxStep, scalAbsoluteTolerance, scalRelativeTolerance);
integ.addStepHandler(new VariableHandler());
double stopTime =
integ.integrate(
pb,
pb.getInitialTime(),
pb.getInitialState(),
pb.getFinalTime(),
new double[pb.getDimension()]);
Assert.assertEquals(pb.getFinalTime(), stopTime, 1.0e-10);
Assert.assertEquals("Dormand-Prince 8 (5, 3)", integ.getName());
}
@Test
public void testKepler()
throws DimensionMismatchException, NumberIsTooSmallException, MaxCountExceededException,
NoBracketingException {
final TestProblem3 pb = new TestProblem3(0.9);
double minStep = 0;
double maxStep = pb.getFinalTime() - pb.getInitialTime();
double scalAbsoluteTolerance = 1.0e-8;
double scalRelativeTolerance = scalAbsoluteTolerance;
FirstOrderIntegrator integ =
new DormandPrince853Integrator(
minStep, maxStep, scalAbsoluteTolerance, scalRelativeTolerance);
integ.addStepHandler(new KeplerHandler(pb));
integ.integrate(
pb,
pb.getInitialTime(),
pb.getInitialState(),
pb.getFinalTime(),
new double[pb.getDimension()]);
Assert.assertEquals(integ.getEvaluations(), pb.getCalls());
Assert.assertTrue(pb.getCalls() < 3300);
}
@Test
public void testBackward()
throws DimensionMismatchException, NumberIsTooSmallException, MaxCountExceededException,
NoBracketingException {
TestProblem5 pb = new TestProblem5();
double minStep = 0;
double maxStep = pb.getFinalTime() - pb.getInitialTime();
double scalAbsoluteTolerance = 1.0e-8;
double scalRelativeTolerance = 0.01 * scalAbsoluteTolerance;
FirstOrderIntegrator integ =
new DormandPrince853Integrator(
minStep, maxStep, scalAbsoluteTolerance, scalRelativeTolerance);
TestProblemHandler handler = new TestProblemHandler(pb, integ);
integ.addStepHandler(handler);
integ.integrate(
pb,
pb.getInitialTime(),
pb.getInitialState(),
pb.getFinalTime(),
new double[pb.getDimension()]);
Assert.assertTrue(handler.getLastError() < 1.1e-7);
Assert.assertTrue(handler.getMaximalValueError() < 1.1e-7);
Assert.assertEquals(0, handler.getMaximalTimeError(), 1.0e-12);
Assert.assertEquals("Dormand-Prince 8 (5, 3)", integ.getName());
}
@Test
public void testUnstableDerivative()
throws DimensionMismatchException, NumberIsTooSmallException, MaxCountExceededException,
NoBracketingException {
final StepProblem stepProblem = new StepProblem(0.0, 1.0, 2.0);
FirstOrderIntegrator integ = new DormandPrince853Integrator(0.1, 10, 1.0e-12, 0.0);
integ.addEventHandler(stepProblem, 1.0, 1.0e-12, 1000);
double[] y = {Double.NaN};
integ.integrate(stepProblem, 0.0, new double[] {0.0}, 10.0, y);
Assert.assertEquals(8.0, y[0], 1.0e-12);
}
@Test
public void testEvents()
throws DimensionMismatchException, NumberIsTooSmallException, MaxCountExceededException,
NoBracketingException {
TestProblem4 pb = new TestProblem4();
double minStep = 0;
double maxStep = pb.getFinalTime() - pb.getInitialTime();
double scalAbsoluteTolerance = 1.0e-9;
double scalRelativeTolerance = 0.01 * scalAbsoluteTolerance;
FirstOrderIntegrator integ =
new DormandPrince853Integrator(
minStep, maxStep, scalAbsoluteTolerance, scalRelativeTolerance);
TestProblemHandler handler = new TestProblemHandler(pb, integ);
integ.addStepHandler(handler);
EventHandler[] functions = pb.getEventsHandlers();
double convergence = 1.0e-8 * maxStep;
for (int l = 0; l < functions.length; ++l) {
integ.addEventHandler(functions[l], Double.POSITIVE_INFINITY, convergence, 1000);
}
Assert.assertEquals(functions.length, integ.getEventHandlers().size());
integ.integrate(
pb,
pb.getInitialTime(),
pb.getInitialState(),
pb.getFinalTime(),
new double[pb.getDimension()]);
Assert.assertEquals(0, handler.getMaximalValueError(), 2.1e-7);
Assert.assertEquals(0, handler.getMaximalTimeError(), convergence);
Assert.assertEquals(12.0, handler.getLastTime(), convergence);
integ.clearEventHandlers();
Assert.assertEquals(0, integ.getEventHandlers().size());
}
private static void computeBeliefBoundaries(
Double hFFPos, Double hFFSpeed, Double hfFFTargetPos, Double hFFCreationTime) {
double currentTime = System.nanoTime() / SEC_NANOSEC_FACTOR;
double[] minBoundaries = new double[1];
double[] maxBoundaries = new double[1];
double startTime = 0.0;
if (hfFFTargetPos != 0.0) {
if (hFFCreationTime > hInit) {
startTime = hFFCreationTime;
hFFPosMin = hFFPos;
hFFPosMax = hFFPos;
hFFSpeedMin = hFFSpeed;
hFFSpeedMax = hFFSpeed;
} else {
if (hFFCreationTime <= hLastTime) {
startTime = hLastTime;
} else if (hFFCreationTime > hLastTime) {
startTime = hFFCreationTime;
hFFPosMin = hFFPos;
hFFPosMax = hFFPos;
hFFSpeedMin = hFFSpeed;
hFFSpeedMax = hFFSpeed;
}
}
// ---------------------- knowledge evaluation --------------------------------
double accMin =
Database.getAcceleration(
hFFSpeedMin, hFFPosMin, Database.lTorques, 0.0, 1.0, Database.lMass);
double accMax =
Database.getAcceleration(
hFFSpeedMax, hFFPosMax, Database.lTorques, 1.0, 0.0, Database.lMass);
FirstOrderIntegrator integrator = new MidpointIntegrator(1);
integrator.setMaxEvaluations((int) TIMEPERIOD);
FirstOrderDifferentialEquations f = new Derivation();
// ------------- min ----------------------
minBoundaries[0] = accMin;
integrator.integrate(f, startTime, minBoundaries, currentTime, minBoundaries);
hFFSpeedMin += minBoundaries[0];
integrator.integrate(f, startTime, minBoundaries, currentTime, minBoundaries);
hFFPosMin += minBoundaries[0];
// ------------- max ----------------------
maxBoundaries[0] = accMax;
integrator.integrate(f, startTime, maxBoundaries, currentTime, maxBoundaries);
hFFSpeedMax += maxBoundaries[0];
integrator.integrate(f, startTime, maxBoundaries, currentTime, maxBoundaries);
hFFPosMax += maxBoundaries[0];
}
if (hFFSpeedMax > 200) hFFSpeedMax = 200.0;
if (hFFSpeedMin < 0.0) hFFSpeedMin = 0.0;
if (hFFPosMin < 0.0) hFFPosMin = 0.0;
hLastTime = currentTime;
hInit = hFFCreationTime;
}
@Test
public void testEventsScheduling() {
FirstOrderDifferentialEquations sincos =
new FirstOrderDifferentialEquations() {
public int getDimension() {
return 2;
}
public void computeDerivatives(double t, double[] y, double[] yDot) {
yDot[0] = y[1];
yDot[1] = -y[0];
}
};
SchedulingChecker sinChecker = new SchedulingChecker(0); // events at 0, PI, 2PI ...
SchedulingChecker cosChecker = new SchedulingChecker(1); // events at PI/2, 3PI/2, 5PI/2 ...
FirstOrderIntegrator integ = new DormandPrince853Integrator(0.001, 1.0, 1.0e-12, 0.0);
integ.addEventHandler(sinChecker, 0.01, 1.0e-7, 100);
integ.addStepHandler(sinChecker);
integ.addEventHandler(cosChecker, 0.01, 1.0e-7, 100);
integ.addStepHandler(cosChecker);
double t0 = 0.5;
double[] y0 = new double[] {FastMath.sin(t0), FastMath.cos(t0)};
double t = 10.0;
double[] y = new double[2];
integ.integrate(sincos, t0, y0, t, y);
}
@Test(expected = NumberIsTooSmallException.class)
public void testMinStep()
throws DimensionMismatchException, NumberIsTooSmallException, MaxCountExceededException,
NoBracketingException {
TestProblem1 pb = new TestProblem1();
double minStep = 0.1 * (pb.getFinalTime() - pb.getInitialTime());
double maxStep = pb.getFinalTime() - pb.getInitialTime();
double[] vecAbsoluteTolerance = {1.0e-15, 1.0e-16};
double[] vecRelativeTolerance = {1.0e-15, 1.0e-16};
FirstOrderIntegrator integ =
new DormandPrince853Integrator(
minStep, maxStep, vecAbsoluteTolerance, vecRelativeTolerance);
TestProblemHandler handler = new TestProblemHandler(pb, integ);
integ.addStepHandler(handler);
integ.integrate(
pb,
pb.getInitialTime(),
pb.getInitialState(),
pb.getFinalTime(),
new double[pb.getDimension()]);
Assert.fail("an exception should have been thrown");
}
// loop through current job/results, assembling dataset
private HashMap<Integer, SpeciesZoneType> genSpeciesDataset(
SimJob job,
EcosystemTimesteps ecosysTimesteps,
Map<Integer, NodeRelationships> ecosysRelationships) {
// calc information relevant to entire ecosystem
int speciesCnt = ecosysTimesteps.getNodeList().size(); // Number of species
int timesteps = ecosysTimesteps.getTimesteps(); // Maximum number of timesteps to run simulation
int timestepsToSave = 0; // Number of timesteps of data to save to output file
int[] matchingTimesteps =
null; // Array of matching timesteps returned by findMatchingTimesteps()
// read in link parameters; this was explicitly configured to allow
// manipulation of link parameter values, but no manipulation is
// performed in this version
LinkParams lPs = new LinkParams(propertiesConfig);
// loop through node values and assemble summary data
int[] speciesID = new int[speciesCnt];
SimJobSZT[] sztArray = new SimJobSZT[speciesCnt];
int spNum = 0;
for (NodeTimesteps nodeTimesteps : ecosysTimesteps.getTimestepMapValues()) {
SimJobSZT sjSzt = job.getSpeciesZoneByNodeId(nodeTimesteps.getNodeId());
sztArray[spNum] = sjSzt;
speciesID[spNum] = sjSzt.getNodeIndex();
spNum++;
}
// define objects to track species' contributions
double[][][] contribs = new double[timesteps][speciesCnt][speciesCnt];
double[][] calcBiomass = new double[timesteps][speciesCnt];
double[][] contribsT; // current timestep
// note: WebServices ATN Model uses B0 with default = 0.5. This presumes
// that biomasses are small, i.e. < 1.0. Division by biomassScale
// here is consistent with usage in WoB_Server.SimulationEngine to
// normalize biomasses.
// need to store bm as it varies over time through integration;
// start with initial bm for each species
double[] currBiomass = new double[speciesCnt];
for (int i = 0; i < speciesCnt; i++) {
NodeTimesteps nodeTimeSteps = ecosysTimesteps.getTimestepMap().get(speciesID[i]);
// manually set biomass vals for excluded initial timesteps; this
// includes the first value to be used as input
currBiomass[i] = nodeTimeSteps.getBiomass(initTimeIdx) / biomassScale;
calcBiomass[0][i] = currBiomass[i];
}
if (Constants.useCommonsMathIntegrator) {
// Use Apache Commons Math GraggBulirschStoerIntegrator
FirstOrderIntegrator integrator =
new GraggBulirschStoerIntegrator(
1.0e-8, // minimal step
100.0, // maximal step
ATNEquations.EXTINCT, // allowed absolute error
1.0e-10); // allowed relative error
// Set up the ATN equations based on the current food web and parameters
ATNEquations ode = new ATNEquations(sztArray, ecosysRelationships, lPs);
ATNEventHandler eventHandler = new ATNEventHandler(ode);
// FIXME: Choose best parameter values
integrator.addEventHandler(
new EventFilter(eventHandler, FilterType.TRIGGER_ONLY_DECREASING_EVENTS),
1, // maximal time interval between switching function checks (this interval prevents
// missing sign changes in case the integration steps becomes very large)
0.0001, // convergence threshold in the event time search
1000, // upper limit of the iteration count in the event time search
new BisectionSolver());
// Set up the StepHandler, which is triggered at each time step by the integrator,
// and copies the current biomass of each species into calcBiomass[timestep].
// See the "Continuous Output" section of
// https://commons.apache.org/proper/commons-math/userguide/ode.html
FixedStepHandler fixedStepHandler =
new FixedStepHandler() {
public void init(double t0, double[] y0, double t) {}
private int timestep = 0;
public void handleStep(double t, double[] y, double[] yDot, boolean isLast) {
// Ensure we don't go past the last time step due to rounding error
if (timestep < calcBiomass.length) {
System.arraycopy(y, 0, calcBiomass[timestep], 0, speciesCnt);
}
timestep++;
}
};
StepHandler stepHandler = new StepNormalizer(timeIntvl, fixedStepHandler);
integrator.addStepHandler(stepHandler);
// Run the integrator to compute the biomass time series
integrator.integrate(ode, 0.0, currBiomass, timeIntvl * timesteps, currBiomass);
if (eventHandler.integrationWasStopped()) {
timestepsToSave = (int) (eventHandler.getTimeStopped() / timeIntvl);
} else {
// Check for an oscillating steady state,
// and only save the data through the first period of the oscillation
matchingTimesteps = findMatchingTimesteps(calcBiomass, timesteps - 1);
System.err.println("\nmatchingTimesteps = " + Arrays.toString(matchingTimesteps));
// Save timesteps up through the second matching timestep,
// or all timesteps if there was no second matching timestep.
if (matchingTimesteps[1] != -1) {
timestepsToSave = matchingTimesteps[1] + 1;
} else {
timestepsToSave = timesteps;
}
}
} else {
// Use BulirschStoerIntegration
// create integration object
boolean isTest = false;
BulirschStoerIntegration bsi =
new BulirschStoerIntegration(
timeIntvl, speciesID, sztArray, ecosysRelationships, lPs, maxBSIErr, equationSet);
// calculate delta-biomass and biomass "contributions" from each related
// species
for (int t = initTimeIdx + 1; t < timesteps; t++) {
boolean success = bsi.performIntegration(time(initTime, t), currBiomass);
if (!success) {
System.out.printf("Integration failed to converge, t = %d\n", t);
System.out.print(bsi.extrapArrayToString(biomassScale));
break;
}
currBiomass = bsi.getYNew();
System.arraycopy(currBiomass, 0, calcBiomass[t], 0, speciesCnt);
contribsT = bsi.getContribs();
for (int i = 0; i < speciesCnt; i++) {
System.arraycopy(contribsT[i], 0, contribs[t - 1][i], 0, speciesCnt);
}
} // timestep loop
}
if (useHDF5) {
saveHDF5OutputFile(
calcBiomass, speciesID, matchingTimesteps, job.getNode_Config(), timestepsToSave);
return null;
}
double[][] webServicesData = new double[speciesCnt][timesteps];
if (Constants.useSimEngine) { // We need the webServicesData only for marginOfErrorCalculation
// extract timestep data from CSV
Functions.extractCSVDataRelns(job.getCsv(), ecosysTimesteps, ecosysRelationships);
spNum = 0;
for (NodeTimesteps nodeTimesteps : ecosysTimesteps.getTimestepMapValues()) {
// copy nodetimestep data to local array for easier access
System.arraycopy(nodeTimesteps.getBiomassArray(), 0, webServicesData[spNum], 0, timesteps);
spNum++;
}
}
// output data
// A. print header
psATN.printf("timesteps");
for (int i = 0; i < timesteps; i++) {
psATN.printf(",%d", i);
}
psATN.println();
/* Convert to CSV String */
String biomassCSV = "";
biomassCSV = "Manipulation_id: " + job.getATNManipulationId() + "\n\n";
int maxTimestep = job.getTimesteps();
// Create Timestep Labels
for (int j = 1; j <= maxTimestep; j++) {
biomassCSV += "," + j;
}
HashMap<Integer, SpeciesZoneType> mSpecies = new HashMap<Integer, SpeciesZoneType>();
// loop through each species
for (int i = 0; i < speciesCnt; i++) {
if (Constants.useSimEngine) {
psATN.printf("i.%d.sim", speciesID[i]);
// B. print WebServices simulation data for species
for (int t = 0; t < timesteps; t++) {
psATN.printf(",%9.0f", webServicesData[i][t]);
}
psATN.println();
}
// B. print combined biomass contributions (i.e. locally calculated biomass)
// for current species.
psATN.printf("i.%d.calc", speciesID[i]);
for (int t = 0; t < timesteps; t++) {
psATN.printf(",%9.0f", calcBiomass[t][i] * biomassScale);
}
psATN.println();
// //C. print individual biomass contributions from other species
// for (int j = 0; j < speciesCnt; j++) {
// psATN.printf("i.%d.j.%d.", speciesID[i], speciesID[j]);
// for (int t = 0; t < timesteps; t++) {
// psATN.printf(",%9.0f", contribs[t][i][j] * biomassScale);
// }
// psATN.println();
// }
float extinction = 1.E-15f;
SimJobSZT sjSzt = job.getSpeciesZoneByNodeId(speciesID[i]);
// add nodes to list in the order that they are received from infos
String name = sjSzt.getName().replaceAll(",", " ") + " [" + sjSzt.getNodeIndex() + "]";
String tempStr = name;
for (int t = 0; t < maxTimestep; t++) {
tempStr += ",";
double biomass = calcBiomass[t][i] * biomassScale;
if (biomass > 0) {
tempStr += biomass > extinction ? Math.ceil(biomass) : 0;
}
if (t == maxTimestep - 1) {
SpeciesZoneType szt = null;
if (!mSpecies.containsKey(sjSzt.getNodeIndex())) {
szt = new SpeciesZoneType(sjSzt.getName(), sjSzt.getNodeIndex(), 0, 0, biomass, null);
mSpecies.put(sjSzt.getNodeIndex(), szt);
} else { // update existing species current biomass
szt = mSpecies.get(sjSzt.getNodeIndex());
szt.setCurrentBiomass(biomass);
}
}
}
biomassCSV += "\n" + tempStr;
}
// Append node config to the ATN CSV
psATN.println();
psATN.println("\"node-config: " + job.getNode_Config() + "\"");
biomassCSV += "\n\n";
biomassCSV += job.getConsumeMap().toString() + "\n\n";
biomassCSV += job.getPathTable().toString();
job.setBiomassCsv(biomassCSV);
// System.out.println(biomassCSV);
return mSpecies;
}
