Examples with Discontinuity cbit.vcell.parser.Discontinuity used on opensource projects

Example 6 with Discontinuity

use of cbit.vcell.parser.Discontinuity in project vcell by virtualcell.

the class FiniteVolumeFileWriter method getDiscontinuityTimes.

private void getDiscontinuityTimes(Vector<Discontinuity> discontinuities, TreeSet<Double> discontinuityTimes) throws ExpressionException, MathException {
    Simulation simulation = simTask.getSimulation();
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    for (Discontinuity discontinuity : discontinuities) {
        Expression rfexp = discontinuity.getRootFindingExp();
        rfexp.bindExpression(simSymbolTable);
        rfexp = simSymbolTable.substituteFunctions(rfexp).flatten();
        String[] symbols = rfexp.getSymbols();
        if (symbols == null) {
            continue;
        }
        boolean bHasT = false;
        for (String symbol : symbols) {
            if (symbol.equals(ReservedVariable.TIME.getName())) {
                bHasT = true;
            }
        }
        if (bHasT) {
            if (symbols.length != 1) {
                throw new ExpressionException(simulation.getSolverTaskDescription().getSolverDescription().getDisplayLabel() + ": time discontinuity " + discontinuity.getDiscontinuityExp().infix() + " can only be a function of time");
            }
            Expression deriv = rfexp.differentiate(ReservedVariable.TIME.getName());
            // we don't allow 5t < 3
            double d = deriv.evaluateConstant();
            if (d != 1 && d != -1) {
                throw new ExpressionException(simulation.getSolverTaskDescription().getSolverDescription().getDisplayLabel() + ": time discontinuity " + discontinuity.getDiscontinuityExp().infix() + " is not allowed.");
            }
            rfexp.substituteInPlace(new Expression(ReservedVariable.TIME.getName()), new Expression(0));
            rfexp.flatten();
            double st = Math.abs(rfexp.evaluateConstant());
            discontinuityTimes.add(st);
        }
    }
/*Simulation simulation = simTask.getSimulation();
	SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
	MonadicFunctionRootFinder rootFinder = new Bisection();
	
	for (Discontinuity discontinuity : discontinuities) {
		Expression rfexp = discontinuity.getRootFindingExp();
		rfexp.bindExpression(simSymbolTable);
		rfexp = simSymbolTable.substituteFunctions(rfexp).flatten();
		String[] symbols = rfexp.getSymbols();
		boolean bHasT = false;
		for (String symbol : symbols) {
			if (symbol.equals(ReservedVariable.TIME.getName())) {
				bHasT = true;
			}
		}
		if (bHasT) {
			if (symbols.length != 1) {
				System.err.println(simulation.getSolverTaskDescription().getSolverDescription().getDisplayLabel() 
						+  ": discontinuity " + discontinuity.getDiscontinuityExp().infix() + " is not just a function of time, not handled properly by solver");
				continue;
			}
		
			double startTime = simulation.getSolverTaskDescription().getTimeBounds().getStartingTime();
			double endTime = simulation.getSolverTaskDescription().getTimeBounds().getEndingTime();
			findAllRoots(rfexp,startTime,endTime,rootFinder,discontinuityTimes,false);
		}
	} ---------------------------------JIM's CODE COMMENTTED FOR FUTURE DEVELOPMENT*/
}

Example 7 with Discontinuity

use of cbit.vcell.parser.Discontinuity in project vcell by virtualcell.

the class OdeFileWriter method writeEvents.

private String writeEvents(HashMap<Discontinuity, String> discontinuityNameMap) throws ExpressionException {
    Simulation simulation = simTask.getSimulation();
    StringBuffer sb = new StringBuffer();
    MathDescription mathDescription = simulation.getMathDescription();
    Iterator<Event> iter = mathDescription.getEvents();
    sb.append("EVENTS " + mathDescription.getNumEvents() + "\n");
    while (iter.hasNext()) {
        Event event = iter.next();
        sb.append("EVENT " + event.getName() + "\n");
        Expression triggerExpression = event.getTriggerExpression();
        triggerExpression = MathUtilities.substituteFunctions(triggerExpression, varsSymbolTable).flatten();
        Vector<Discontinuity> v = triggerExpression.getDiscontinuities();
        for (Discontinuity od : v) {
            od = getSubsitutedAndFlattened(od, varsSymbolTable);
            String dname = discontinuityNameMap.get(od);
            if (dname == null) {
                dname = ROOT_VARIABLE_PREFIX + discontinuityNameMap.size();
                discontinuityNameMap.put(od, dname);
            }
            triggerExpression.substituteInPlace(od.getDiscontinuityExp(), new Expression("(" + dname + "==1)"));
        }
        sb.append("TRIGGER " + triggerExpression.infix() + ";\n");
        Delay delay = event.getDelay();
        if (delay != null) {
            Expression durationExpression = delay.getDurationExpression();
            durationExpression = MathUtilities.substituteFunctions(durationExpression, varsSymbolTable).flatten();
            sb.append("DELAY " + delay.useValuesFromTriggerTime() + " " + durationExpression.infix() + ";\n");
        }
        sb.append("EVENTASSIGNMENTS " + event.getNumEventAssignments() + "\n");
        Iterator<EventAssignment> iter2 = event.getEventAssignments();
        while (iter2.hasNext()) {
            EventAssignment eventAssignment = iter2.next();
            Expression assignmentExpression = eventAssignment.getAssignmentExpression();
            assignmentExpression = MathUtilities.substituteFunctions(assignmentExpression, varsSymbolTable).flatten();
            Variable assignmentTarget = eventAssignment.getVariable();
            for (int i = 0; i < fieldStateVariables.size(); i++) {
                if (assignmentTarget.getName().equals(fieldStateVariables.get(i).getVariable().getName())) {
                    sb.append(i + " " + assignmentExpression.infix() + ";\n");
                    break;
                }
            }
        }
    }
    return sb.toString();
}

Example 8 with Discontinuity

use of cbit.vcell.parser.Discontinuity in project vcell by virtualcell.

the class OdeFileWriter method write.

/**
 * Insert the method's description here.
 * Creation date: (3/8/00 10:31:52 PM)
 */
public void write(String[] parameterNames) throws Exception {
    createStateVariables();
    createSymbolTable();
    Simulation simulation = simTask.getSimulation();
    if (simulation.getSolverTaskDescription().getUseSymbolicJacobian()) {
        throw new RuntimeException("symbolic jacobian option not yet supported in interpreted Stiff solver");
    }
    writeJMSParamters();
    SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
    TimeBounds timeBounds = solverTaskDescription.getTimeBounds();
    ErrorTolerance errorTolerance = solverTaskDescription.getErrorTolerance();
    printWriter.println("SOLVER " + getSolverName());
    printWriter.println("STARTING_TIME " + timeBounds.getStartingTime());
    printWriter.println("ENDING_TIME " + timeBounds.getEndingTime());
    printWriter.println("RELATIVE_TOLERANCE " + errorTolerance.getRelativeErrorTolerance());
    printWriter.println("ABSOLUTE_TOLERANCE " + errorTolerance.getAbsoluteErrorTolerance());
    printWriter.println("MAX_TIME_STEP " + simulation.getSolverTaskDescription().getTimeStep().getMaximumTimeStep());
    OutputTimeSpec ots = simulation.getSolverTaskDescription().getOutputTimeSpec();
    if (ots.isDefault()) {
        printWriter.println("KEEP_EVERY " + ((DefaultOutputTimeSpec) ots).getKeepEvery());
    } else if (ots.isUniform()) {
        printWriter.println("OUTPUT_TIME_STEP " + ((UniformOutputTimeSpec) ots).getOutputTimeStep());
    } else if (ots.isExplicit()) {
        printWriter.println("OUTPUT_TIMES " + ((ExplicitOutputTimeSpec) ots).getNumTimePoints());
        printWriter.println(((ExplicitOutputTimeSpec) ots).toSpaceSeperatedMultiLinesOfString());
    }
    if (parameterNames != null && parameterNames.length != 0) {
        printWriter.println("NUM_PARAMETERS " + parameterNames.length);
        for (int i = 0; i < parameterNames.length; i++) {
            printWriter.println(parameterNames[i]);
        }
    }
    HashMap<Discontinuity, String> discontinuityNameMap = new HashMap<Discontinuity, String>();
    String eventString = null;
    if (simulation.getMathDescription().hasEvents()) {
        eventString = writeEvents(discontinuityNameMap);
    }
    String equationString = writeEquations(discontinuityNameMap);
    if (discontinuityNameMap.size() > 0) {
        printWriter.println("DISCONTINUITIES " + discontinuityNameMap.size());
        for (Discontinuity od : discontinuityNameMap.keySet()) {
            printWriter.println(discontinuityNameMap.get(od) + " " + od.getDiscontinuityExp().flatten().infix() + "; " + od.getRootFindingExp().flatten().infix() + ";");
        }
    }
    if (eventString != null) {
        printWriter.print(eventString);
    }
    printWriter.println("NUM_EQUATIONS " + getStateVariableCount());
    printWriter.println(equationString);
}