Examples with MathDescription cbit.vcell.math.MathDescription used on opensource projects

Example 96 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class OutputFunctionContext method propertyChange.

public void propertyChange(java.beans.PropertyChangeEvent event) {
    if (event.getSource() == simulationOwner && event.getPropertyName().equals("mathDescription")) {
        rebindAll();
    }
    if (event.getPropertyName().equals("geometry")) {
        Geometry oldGeometry = (Geometry) event.getOldValue();
        Geometry newGeometry = (Geometry) event.getNewValue();
        // changing from ode to pde
        if (oldGeometry != null && oldGeometry.getDimension() == 0 && newGeometry.getDimension() > 0) {
            ArrayList<AnnotatedFunction> newFuncList = new ArrayList<AnnotatedFunction>();
            for (AnnotatedFunction function : outputFunctionsList) {
                try {
                    Expression newexp = new Expression(function.getExpression());
                    // making sure that output function is not direct function of constant.
                    newexp.bindExpression(this);
                    // here use math description as symbol table because we allow
                    // new expression itself to be function of constant.
                    MathDescription mathDescription = getSimulationOwner().getMathDescription();
                    newexp = MathUtilities.substituteFunctions(newexp, mathDescription).flatten();
                    VariableType newFuncType = VariableType.VOLUME;
                    String[] symbols = newexp.getSymbols();
                    if (symbols != null) {
                        // figure out the function type
                        VariableType[] varTypes = new VariableType[symbols.length];
                        for (int i = 0; i < symbols.length; i++) {
                            Variable var = mathDescription.getVariable(symbols[i]);
                            varTypes[i] = VariableType.getVariableType(var);
                        }
                        // check with flattened expression to find out the variable type of the new expression
                        Function flattenedFunction = new Function(function.getName(), newexp, function.getDomain());
                        newFuncType = SimulationSymbolTable.getFunctionVariableType(flattenedFunction, getSimulationOwner().getMathDescription(), symbols, varTypes, true);
                    }
                    AnnotatedFunction newFunc = new AnnotatedFunction(function.getName(), function.getExpression(), function.getDomain(), "", newFuncType, FunctionCategory.OUTPUTFUNCTION);
                    newFuncList.add(newFunc);
                    newFunc.bind(this);
                } catch (ExpressionException ex) {
                    ex.printStackTrace();
                    throw new RuntimeException(ex.getMessage());
                } catch (InconsistentDomainException ex) {
                    ex.printStackTrace();
                    throw new RuntimeException(ex.getMessage());
                }
            }
            try {
                setOutputFunctions0(newFuncList);
            } catch (PropertyVetoException e) {
                e.printStackTrace();
                throw new RuntimeException(e.getMessage());
            }
        }
    }
}

Example 97 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class OutputFunctionContext method getEntry.

public SymbolTableEntry getEntry(java.lang.String identifierString) {
    // 
    // use MathDescription as the primary SymbolTable, just replace the Constants with the overrides.
    // 
    SymbolTableEntry ste = null;
    MathDescription mathDescription = simulationOwner.getMathDescription();
    if (mathDescription != null) {
        ste = mathDescription.getEntry(identifierString);
        if (ste != null && !(ste instanceof PseudoConstant) && !(ste instanceof Constant)) {
            return ste;
        }
        ste = mathDescription.getPostProcessingBlock().getDataGenerator(identifierString);
        if (ste instanceof DataGenerator) {
            return ste;
        }
    }
    // see if it is an output function.
    ste = getOutputFunction(identifierString);
    return ste;
}

Example 98 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class Simulation method propertyChange.

public void propertyChange(PropertyChangeEvent evt) {
    MathDescription md = getMathDescription();
    boolean bIsMath = evt.getSource() == md;
    if (bIsMath && evt.getPropertyName().equals("geometry")) {
        try {
            refreshMeshSpec();
        } catch (PropertyVetoException e) {
            e.printStackTrace();
            throw new RuntimeException(e.getMessage(), e);
        }
    }
}

Example 99 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class DefaultODESolver method createStateVariables.

/**
 * This method was created in VisualAge.
 */
private Vector<StateVariable> createStateVariables() throws MathException, ExpressionException {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    Simulation sim = simSymbolTable.getSimulation();
    Vector<StateVariable> stateVariables = new Vector<StateVariable>();
    // get Ode's from MathDescription and create ODEStateVariables
    Enumeration<Equation> enum1 = getSubDomain().getEquations();
    while (enum1.hasMoreElements()) {
        Equation equation = enum1.nextElement();
        if (equation instanceof OdeEquation) {
            stateVariables.addElement(new ODEStateVariable((OdeEquation) equation, simSymbolTable));
        } else {
            throw new MathException("encountered non-ode equation, unsupported");
        }
    }
    MathDescription mathDescription = sim.getMathDescription();
    if (rateSensitivity == null) {
        rateSensitivity = new RateSensitivity(mathDescription, mathDescription.getSubDomains().nextElement());
    }
    if (jacobian == null) {
        jacobian = new Jacobian(mathDescription, mathDescription.getSubDomains().nextElement());
    }
    // get Jacobian and RateSensitivities from MathDescription and create SensStateVariables
    for (int v = 0; v < fieldSensVariables.size(); v++) {
        stateVariables.addElement(new SensStateVariable(fieldSensVariables.elementAt(v), rateSensitivity, jacobian, fieldSensVariables, simSymbolTable));
    }
    if (stateVariables.size() == 0) {
        throw new MathException("there are no equations defined");
    }
    return (stateVariables);
}

Example 100 with MathDescription

use of cbit.vcell.math.MathDescription 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();
}