OdeSolver.java
/*
* Copyright 2013 University of Glasgow.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package broadwick.odesolver;
import com.google.common.collect.Table;
import com.google.common.collect.TreeBasedTable;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import lombok.Getter;
import lombok.Setter;
import lombok.Synchronized;
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.lang3.StringUtils;
/**
* A base class for all ODE solvers.
*/
@Slf4j
public abstract class OdeSolver {
/**
* Create the solver object with initial consitions.
* @param ode the ode object containing the specification of the ode.
* @param tStart the start time (the independent variable is assumed to be time)
* @param tEnd the end time (the independent variable is assumed to be time)
* @param stepSize the size of the step to be used in the solver.
*/
public OdeSolver(final Ode ode, final double tStart, final double tEnd, final double stepSize) {
this.ode = ode;
this.independentVariableStart = tStart;
this.independentVariableEnd = tEnd;
this.stepSize = stepSize;
this.thetaQueue = new ThetaQueue();
dependentVariables = new ArrayList<>(ode.getInitialValues());
log.debug("Created ODE solver");
}
/**
* Add an observer to the engines list of observers.
* @param observer the observer.
*/
public final void addObserver(final Observer observer) {
if (observer.getSolver() != this) {
log.error("Cannot add Observer to OdeSolver, type = {}", observer.getSolver());
throw new IllegalArgumentException("Observer doesn't belong to this solver!");
}
log.trace("Adding Observer to OdeSolver");
this.getObservers().add(observer);
}
/**
* Register a new theta event that is triggered at a given time.
* @param obs the observers which is registering.
* @param thetaTime the time the theta event occurs.
* @param event the theta event.
*/
public final void registerNewTheta(final Observer obs, final double thetaTime, final Object event) {
thetaQueue.pushTheta(thetaTime, obs, event);
}
/**
* Gets called when the simulator reaches the predetermined time of a theta event. All the observers for the events
* that are configured for this time are notified and given a list of events that are triggered.
*/
protected final void doThetaEvent() {
final double nextThetaEventTime = thetaQueue.getNextThetaEventTime();
final Map<Observer, Collection<Object>> nextEvents = thetaQueue.getNextEventDataAndRemove();
for (Map.Entry<Observer, Collection<Object>> entry : nextEvents.entrySet()) {
final Observer observer = entry.getKey();
final Collection<Object> events = entry.getValue();
if (events != null) {
log.trace("Informing observer of {} theta events", events.size());
observer.theta(nextThetaEventTime, events);
}
}
log.trace("Finished theta events next = {}", thetaQueue.getNextThetaEventTime());
}
/**
* Theta defines a moment, where the simulator has to invoke <TT>theta</TT> of a observers. It is used e.g. to
* determine the amounts of species at one moments. Extending class just have to call
* {@link Simulator#doThetaEvent()} which basically calls the observers.
* @return the theta
*/
public final double getNextThetaEventTime() {
return thetaQueue.getNextThetaEventTime();
}
/**
* Get a csv representation of the current state of the dependent variables.
* @return a csv string.
*/
public final String getDependetVariablesAsCsv() {
return StringUtils.join(dependentVariables, ",");
}
/**
* Get the dependent variables.
* @return an array of the dependent variables.
*/
public final List<Double> getDependentVariables() {
return dependentVariables;
}
/**
* Solve the system of ODEs.
*/
public abstract void run();
/**
* Manages the registered theta events. Each registered theta event is stored in a table containing the time of the
* event the list of observers for that event and the list of events for that time.
*/
private static class ThetaQueue {
/**
* Construct an empty theta queue.
*/
public ThetaQueue() {
thetas = TreeBasedTable.create();
}
/**
* Add a new theta event to the registry, including the time, collection of observers and collection of events.
* Each event is stored as an object where it is assumed that the observer
* @param time the time the theta event occurs.
* @param obs the observers.
* @param theta the theta event.
*/
@Synchronized
public void pushTheta(final double time, final Observer obs, final Object theta) {
log.trace("Adding new {} theta event at t={}", theta.getClass(), time);
Collection<Object> events = thetas.get(time, obs);
if (events == null) {
try {
log.trace("No theta events registered at t={}; Creating new list", time);
events = new HashSet<>();
events.add(theta);
thetas.put(time, obs, events);
} catch (UnsupportedOperationException | ClassCastException |
IllegalArgumentException | IllegalStateException e) {
log.error("Could not register theta. {}", e.getLocalizedMessage());
}
} else {
log.trace("Found {} theta events for t={}; Adding new event", events.size(), time);
events.add(theta);
}
// Now we need to update the nextThetaEventTime
if (thetas.rowKeySet().isEmpty()) {
nextThetaEventTime = Double.POSITIVE_INFINITY;
} else {
nextThetaEventTime = Collections.min(thetas.rowKeySet());
}
}
/**
* Get the next observer and the collection of events they are subscribed to and remove it from the theta queue.
* @return a map of the observers and their subscribed data.
*/
public Map<Observer, Collection<Object>> getNextEventDataAndRemove() {
final Map<Observer, Collection<Object>> nextEventData = thetas.row(nextThetaEventTime);
// we have a view of the underlying data that we want to return, copy it first then delete the
// underlying data.
final Map<Observer, Collection<Object>> eventData = new HashMap<>(nextEventData);
log.trace("Found {} configured events and observers at t={}", eventData.size(), nextThetaEventTime);
for (Observer obs : eventData.keySet()) {
final Collection<Object> removed = thetas.remove(nextThetaEventTime, obs);
log.trace("Removed {} items from registered theta list", removed.size());
}
// Now we need to update the nextThetaEventTime
if (thetas.rowKeySet().isEmpty()) {
nextThetaEventTime = Double.POSITIVE_INFINITY;
} else {
nextThetaEventTime = Collections.min(thetas.rowKeySet());
}
return eventData;
}
@Getter
private final Table<Double, Observer, Collection<Object>> thetas;
@Getter
private double nextThetaEventTime;
}
protected final List<Double> dependentVariables;
protected final double stepSize;
@Getter
@SuppressWarnings("PMD.UnusedPrivateField")
private final Double independentVariableStart;
@Getter
@SuppressWarnings("PMD.UnusedPrivateField")
private final Double independentVariableEnd;
@Getter
@SuppressWarnings("PMD.UnusedPrivateField")
private final Ode ode;
@Getter
@SuppressWarnings("PMD.UnusedPrivateField")
protected double currentTime = 0;
@Getter
@Setter
@SuppressWarnings("PMD.UnusedPrivateField")
private OdeController controller = new DefaultOdeController(100.0);
@Getter
@SuppressWarnings("PMD.UnusedPrivateField")
private final Set<Observer> observers = new HashSet<>(1);
private ThetaQueue thetaQueue;
}