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Example 26 with Constant

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

the class RateSensitivity method makeCP.

/**
 * This method was created by a SmartGuide.
 * @param rateIndex int
 * @param varIndex int
 * @param exp cbit.vcell.parser.Expression
 * @exception java.lang.Exception The exception description.
 */
private void makeCP(int rateIndex, int constantIndex) throws ExpressionException, ArrayIndexOutOfBoundsException {
    if (rateIndex < 0 || rateIndex >= numRates) {
        throw new ArrayIndexOutOfBoundsException("rateIndex out of range '" + rateIndex + "'");
    }
    if (constantIndex < 0 || constantIndex >= numConstants) {
        throw new ArrayIndexOutOfBoundsException("constantIndex out of range '" + constantIndex + "'");
    }
    Expression rateExp = rates[rateIndex];
    Constant constant = consts[constantIndex];
    rateExp.bindExpression(mathDesc);
    Expression diff = rateExp.differentiate(constant.getName());
    diff.bindExpression(null);
    diff = diff.flatten();
    diff.bindExpression(mathDesc);
    CPexp[rateIndex + constantIndex * numRates] = diff;
}
Also used : Expression(cbit.vcell.parser.Expression) Constant(cbit.vcell.math.Constant)

Example 27 with Constant

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

the class SundialsSolver method getSensitivityParameter.

/**
 * Insert the method's description here.
 * Creation date: (6/27/2001 12:22:10 PM)
 * @return int
 */
public Constant getSensitivityParameter() {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    Constant origSensParam = simSymbolTable.getSimulation().getSolverTaskDescription().getSensitivityParameter();
    // 
    if (origSensParam != null) {
        return (Constant) simSymbolTable.getVariable(origSensParam.getName());
    } else {
        return null;
    }
}
Also used : Constant(cbit.vcell.math.Constant) SimulationSymbolTable(cbit.vcell.solver.SimulationSymbolTable)

Example 28 with Constant

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

the class OdeFileWriter method createStateVariables.

private void createStateVariables() throws Exception {
    Simulation simulation = simTask.getSimulation();
    MathDescription mathDescription = simulation.getMathDescription();
    SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
    // get Ode's from MathDescription and create ODEStateVariables
    Enumeration<Equation> enum1 = mathDescription.getSubDomains().nextElement().getEquations();
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    while (enum1.hasMoreElements()) {
        Equation equation = enum1.nextElement();
        if (equation instanceof OdeEquation) {
            fieldStateVariables.addElement(new ODEStateVariable((OdeEquation) equation, simSymbolTable));
        } else {
            throw new MathException("encountered non-ode equation, unsupported");
        }
    }
    // Get sensitivity variables
    Variable[] variables = simSymbolTable.getVariables();
    Vector<SensVariable> sensVariables = new Vector<SensVariable>();
    Constant sensitivityParameter = solverTaskDescription.getSensitivityParameter();
    if (sensitivityParameter != null) {
        Constant origSensParam = sensitivityParameter;
        Constant overriddenSensParam = (Constant) simSymbolTable.getVariable(origSensParam.getName());
        for (int i = 0; i < variables.length; i++) {
            if (variables[i] instanceof VolVariable) {
                VolVariable volVariable = (VolVariable) variables[i];
                SensVariable sv = new SensVariable(volVariable, overriddenSensParam);
                sensVariables.addElement(sv);
            }
        }
    }
    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 < sensVariables.size(); v++) {
        fieldStateVariables.addElement(new SensStateVariable(sensVariables.elementAt(v), rateSensitivity, jacobian, sensVariables, simSymbolTable));
    }
}
Also used : ReservedVariable(cbit.vcell.math.ReservedVariable) ParameterVariable(cbit.vcell.math.ParameterVariable) Variable(cbit.vcell.math.Variable) VolVariable(cbit.vcell.math.VolVariable) MathDescription(cbit.vcell.math.MathDescription) VolVariable(cbit.vcell.math.VolVariable) Constant(cbit.vcell.math.Constant) SimulationSymbolTable(cbit.vcell.solver.SimulationSymbolTable) OdeEquation(cbit.vcell.math.OdeEquation) Equation(cbit.vcell.math.Equation) Simulation(cbit.vcell.solver.Simulation) OdeEquation(cbit.vcell.math.OdeEquation) MathException(cbit.vcell.math.MathException) SolverTaskDescription(cbit.vcell.solver.SolverTaskDescription) Vector(java.util.Vector)

Example 29 with Constant

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

the class SimulationData method getVarAndFunctionDataIdentifiers.

/**
 * This method was created in VisualAge.
 * @return java.lang.String[]
 */
public synchronized DataIdentifier[] getVarAndFunctionDataIdentifiers(OutputContext outputContext) throws IOException, DataAccessException {
    // Is this zip format?
    boolean bIsChombo = false;
    try {
        bIsChombo = isChombo();
    } catch (FileNotFoundException e) {
        e.printStackTrace(System.out);
    }
    File zipFile1 = getZipFile(bIsChombo, null);
    File zipFile2 = getZipFile(bIsChombo, 0);
    bZipFormat1 = false;
    bZipFormat2 = false;
    if (zipFile1.exists()) {
        bZipFormat1 = true;
    } else if (zipFile2.exists()) {
        bZipFormat2 = true;
    }
    refreshLogFile();
    if (!isComsol()) {
        try {
            refreshMeshFile();
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
    }
    if (!isRulesData && !getIsODEData() && !isComsol() && dataFilenames != null) {
        // read variables only when I have never read the file since variables don't change
        if (dataSetIdentifierList.size() == 0) {
            File file = getPDEDataFile(0.0);
            DataSet dataSet = getPDEDataSet(file, 0.0);
            String[] varNames = dataSet.getDataNames();
            int[] varTypeInts = dataSet.getVariableTypeIntegers();
            if (varNames == null) {
                return null;
            }
            dataSetIdentifierList.clear();
            for (int i = 0; i < varNames.length; i++) {
                VariableType varType = null;
                try {
                    varType = VariableType.getVariableTypeFromInteger(varTypeInts[i]);
                } catch (IllegalArgumentException e) {
                    if (LG.isEnabledFor(Level.WARN)) {
                        LG.warn("Exception typing " + varNames[i] + " has unsupported type " + varTypeInts[i] + ": " + e.getMessage());
                    }
                    varType = SimulationData.getVariableTypeFromLength(mesh, dataSet.getDataLength(varNames[i]));
                }
                Domain domain = Variable.getDomainFromCombinedIdentifier(varNames[i]);
                String varName = Variable.getNameFromCombinedIdentifier(varNames[i]);
                dataSetIdentifierList.addElement(new DataSetIdentifier(varName, varType, domain));
            }
            refreshDataProcessingOutputInfo(outputContext);
            if (dataProcessingOutputInfo != null) {
                for (int i = 0; i < dataProcessingOutputInfo.getVariableNames().length; i++) {
                    if (dataProcessingOutputInfo.getPostProcessDataType(dataProcessingOutputInfo.getVariableNames()[i]).equals(DataProcessingOutputInfo.PostProcessDataType.image)) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(dataProcessingOutputInfo.getVariableNames()[i], VariableType.POSTPROCESSING, null));
                    }
                }
            }
        }
        // always read functions file since functions might change
        getFunctionDataIdentifiers(outputContext);
    }
    if ((isRulesData || getIsODEData()) && dataSetIdentifierList.size() == 0) {
        ODEDataBlock odeDataBlock = getODEDataBlock();
        if (odeDataBlock == null) {
            throw new DataAccessException("Results are not availabe yet. Please try again later.");
        }
        ODESimData odeSimData = odeDataBlock.getODESimData();
        int colCount = odeSimData.getColumnDescriptionsCount();
        // assume index=0 is time "t"
        int DATA_OFFSET = 1;
        dataSetIdentifierList.clear();
        for (int i = 0; i < (colCount - DATA_OFFSET); i++) {
            String varName = odeSimData.getColumnDescriptions(i + DATA_OFFSET).getDisplayName();
            // TODO domain
            Domain domain = null;
            dataSetIdentifierList.addElement(new DataSetIdentifier(varName, VariableType.NONSPATIAL, domain));
        }
    }
    if (isComsol() && dataSetIdentifierList.size() == 0) {
        ComsolSimFiles comsolSimFiles = getComsolSimFiles();
        if (comsolSimFiles.simTaskXMLFile != null) {
            try {
                String xmlString = FileUtils.readFileToString(comsolSimFiles.simTaskXMLFile);
                SimulationTask simTask = XmlHelper.XMLToSimTask(xmlString);
                Enumeration<Variable> variablesEnum = simTask.getSimulation().getMathDescription().getVariables();
                while (variablesEnum.hasMoreElements()) {
                    Variable var = variablesEnum.nextElement();
                    if (var instanceof VolVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.VOLUME, var.getDomain()));
                    } else if (var instanceof MemVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.MEMBRANE, var.getDomain()));
                    } else if (var instanceof Function) {
                        VariableType varType = VariableType.UNKNOWN;
                        if (var.getDomain() != null && var.getDomain().getName() != null) {
                            SubDomain subDomain = simTask.getSimulation().getMathDescription().getSubDomain(var.getDomain().getName());
                            if (subDomain instanceof CompartmentSubDomain) {
                                varType = VariableType.VOLUME;
                            } else if (subDomain instanceof MembraneSubDomain) {
                                varType = VariableType.MEMBRANE;
                            } else if (subDomain instanceof FilamentSubDomain) {
                                throw new RuntimeException("filament subdomains not supported");
                            } else if (subDomain instanceof PointSubDomain) {
                                varType = VariableType.POINT_VARIABLE;
                            }
                        }
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), varType, var.getDomain()));
                    } else if (var instanceof Constant) {
                        System.out.println("ignoring Constant " + var.getName());
                    } else if (var instanceof InsideVariable) {
                        System.out.println("ignoring InsideVariable " + var.getName());
                    } else if (var instanceof OutsideVariable) {
                        System.out.println("ignoring OutsideVariable " + var.getName());
                    } else {
                        throw new RuntimeException("unexpected variable " + var.getName() + " of type " + var.getClass().getName());
                    }
                }
            } catch (XmlParseException | ExpressionException e) {
                e.printStackTrace();
                throw new RuntimeException("failed to read sim task file, msg: " + e.getMessage(), e);
            }
        }
    }
    DataIdentifier[] dis = new DataIdentifier[dataSetIdentifierList.size()];
    for (int i = 0; i < dataSetIdentifierList.size(); i++) {
        DataSetIdentifier dsi = (DataSetIdentifier) dataSetIdentifierList.elementAt(i);
        String displayName = dsi.getName();
        if (dsi.isFunction()) {
            AnnotatedFunction f = null;
            for (int j = 0; j < annotatedFunctionList.size(); j++) {
                AnnotatedFunction function = (AnnotatedFunction) annotatedFunctionList.elementAt(j);
                if (function.getName().equals(dsi.getName())) {
                    f = function;
                    break;
                }
            }
            if (f != null) {
                displayName = f.getDisplayName();
            }
        }
        dis[i] = new DataIdentifier(dsi.getName(), dsi.getVariableType(), dsi.getDomain(), dsi.isFunction(), displayName);
    }
    return dis;
}
Also used : MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) SimulationTask(cbit.vcell.messaging.server.SimulationTask) InsideVariable(cbit.vcell.math.InsideVariable) VolVariable(cbit.vcell.math.VolVariable) ReservedVariable(cbit.vcell.math.ReservedVariable) MemVariable(cbit.vcell.math.MemVariable) OutsideVariable(cbit.vcell.math.OutsideVariable) Variable(cbit.vcell.math.Variable) VCDataIdentifier(org.vcell.util.document.VCDataIdentifier) VCSimulationDataIdentifier(cbit.vcell.solver.VCSimulationDataIdentifier) ExternalDataIdentifier(org.vcell.util.document.ExternalDataIdentifier) Constant(cbit.vcell.math.Constant) FileNotFoundException(java.io.FileNotFoundException) PointSubDomain(cbit.vcell.math.PointSubDomain) ODESimData(cbit.vcell.solver.ode.ODESimData) InsideVariable(cbit.vcell.math.InsideVariable) ExpressionException(cbit.vcell.parser.ExpressionException) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) FilamentSubDomain(cbit.vcell.math.FilamentSubDomain) SubDomain(cbit.vcell.math.SubDomain) PointSubDomain(cbit.vcell.math.PointSubDomain) MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) Function(cbit.vcell.math.Function) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction) MemVariable(cbit.vcell.math.MemVariable) DataAccessException(org.vcell.util.DataAccessException) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction) ComsolSimFiles(org.vcell.vis.io.ComsolSimFiles) VariableType(cbit.vcell.math.VariableType) VolVariable(cbit.vcell.math.VolVariable) XmlParseException(cbit.vcell.xml.XmlParseException) FilamentSubDomain(cbit.vcell.math.FilamentSubDomain) MathException(cbit.vcell.math.MathException) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) OutsideVariable(cbit.vcell.math.OutsideVariable) CompartmentSubDomain(cbit.vcell.math.CompartmentSubDomain) FilamentSubDomain(cbit.vcell.math.FilamentSubDomain) SubDomain(cbit.vcell.math.SubDomain) PointSubDomain(cbit.vcell.math.PointSubDomain) Domain(cbit.vcell.math.Variable.Domain) MembraneSubDomain(cbit.vcell.math.MembraneSubDomain) ZipFile(org.apache.commons.compress.archivers.zip.ZipFile) File(java.io.File)

Example 30 with Constant

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

the class ConstantArraySpec method createIntervalSpec.

/**
 * Insert the method's description here.
 * Creation date: (9/23/2005 1:47:17 PM)
 * @return cbit.vcell.solver.ConstantArraySpec
 * @param name java.lang.String
 * @param minValue double
 * @param maxValue double
 * @param numValues int
 * @param logInterval boolean
 */
public static ConstantArraySpec createIntervalSpec(String name, double minValue, double maxValue, int numValues, boolean logInterval) {
    if (logInterval && (minValue * maxValue <= 0))
        throw new RuntimeException("Min and Max values cannot be zero or have different signs for log interval");
    ConstantArraySpec spec = new ConstantArraySpec();
    spec.type = TYPE_INTERVAL;
    spec.name = name;
    spec.minValue = minValue;
    spec.maxValue = maxValue;
    spec.numValues = numValues;
    spec.logInterval = logInterval;
    spec.constants = new Constant[numValues];
    if (logInterval) {
        for (int i = 0; i < numValues; i++) {
            spec.constants[i] = new Constant(name, new cbit.vcell.parser.Expression(minValue * Math.pow(maxValue / minValue, ((double) i) / (numValues - 1))));
        }
    } else {
        for (int i = 0; i < numValues; i++) {
            spec.constants[i] = new Constant(name, new cbit.vcell.parser.Expression(minValue + (maxValue - minValue) * ((double) i) / (numValues - 1)));
        }
    }
    return spec;
}
Also used : Expression(cbit.vcell.parser.Expression) Constant(cbit.vcell.math.Constant)

Aggregations

Constant (cbit.vcell.math.Constant)69 Expression (cbit.vcell.parser.Expression)43 Variable (cbit.vcell.math.Variable)31 Function (cbit.vcell.math.Function)24 MathDescription (cbit.vcell.math.MathDescription)22 VolVariable (cbit.vcell.math.VolVariable)21 ExpressionException (cbit.vcell.parser.ExpressionException)21 MathException (cbit.vcell.math.MathException)15 Vector (java.util.Vector)15 CompartmentSubDomain (cbit.vcell.math.CompartmentSubDomain)14 MemVariable (cbit.vcell.math.MemVariable)14 MembraneRegionVariable (cbit.vcell.math.MembraneRegionVariable)13 SubDomain (cbit.vcell.math.SubDomain)13 MacroscopicRateConstant (cbit.vcell.math.MacroscopicRateConstant)12 VolumeRegionVariable (cbit.vcell.math.VolumeRegionVariable)12 ReservedVariable (cbit.vcell.math.ReservedVariable)11 FilamentVariable (cbit.vcell.math.FilamentVariable)10 InsideVariable (cbit.vcell.math.InsideVariable)10 OutsideVariable (cbit.vcell.math.OutsideVariable)10 FilamentRegionVariable (cbit.vcell.math.FilamentRegionVariable)9