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

Example 26 with MathException

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

the class StochFileWriter method initialize.

/**
 * Get infomation for stochasic input file.
 * Validate the information. If it is valid, a true value will be return.
 * The function will be called by writeStochInputFile().
 * Creation date: (6/23/2006 3:59:34 PM)
 * @return boolean
 */
public void initialize() throws Exception {
    Simulation simulation = simTask.getSimulation();
    // check variables
    if (!simulation.getMathDescription().getVariables().hasMoreElements()) {
        throw new MathException("Stochastic model has no variable.");
    }
    // check subDomain
    SubDomain subDomain = null;
    Enumeration<SubDomain> e = simulation.getMathDescription().getSubDomains();
    if (e.hasMoreElements()) {
        subDomain = e.nextElement();
    } else
        throw new MathException("There is no sub domain.");
    // check jump processes
    if (subDomain.getJumpProcesses().size() < 1) {
        throw new MathException("Stochastic model has no jump process.");
    }
}

Example 27 with MathException

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

the class NetCDFWriter method initialize.

/**
 * Extract infomation from simulation to write hybrid input file.
 * Validate the information. If it is valid, a true value will be return.
 * The function will be called by writeHybridInputFile().
 * Creation date: (5/22/2007 3:59:34 PM)
 * @return boolean
 */
public boolean initialize() throws Exception {
    Simulation simulation = simTask.getSimulation();
    // check variables
    if (!simulation.getMathDescription().getVariables().hasMoreElements()) {
        throw new MathException("Stochastic model has no variable.");
    }
    // check subDomain
    SubDomain subDomain = null;
    Enumeration<SubDomain> e = simulation.getMathDescription().getSubDomains();
    if (e.hasMoreElements()) {
        subDomain = e.nextElement();
    } else
        throw new MathException("There is no sub domain.");
    // check jump processes
    if (subDomain.getJumpProcesses().size() < 1) {
        throw new MathException("Stochastic model has no jump process.");
    }
    return true;
}

Example 28 with MathException

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

the class NetCDFWriter method getReactionRateLaws.

/**
 * @param reacs
 * @return ReactionRateLaw[]
 */
private ReactionRateLaw[] getReactionRateLaws(Expression[] probs) throws ExpressionException, MathException {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    ReactionRateLaw[] results = new ReactionRateLaw[probs.length];
    varInProbOrderHash = new Hashtable[probs.length];
    for (int i = 0; i < probs.length; i++) {
        varInProbOrderHash[i] = new Hashtable<String, Integer>();
        results[i] = new ReactionRateLaw();
        Expression prob = probs[i];
        String[] symbols = prob.getSymbols();
        // get stoch variables involved in the reaction
        String[] varSymbols = getVariableSymbols(symbols);
        // max allowed order for each variable(species)
        int maxOrder = 5;
        // order of the reaction
        int totalOrder = 0;
        // the expression of the rate constant
        Expression coefExp = null;
        if (symbols != null) {
            if ((varSymbols != null && !Compare.isEqual(symbols, varSymbols)) || varSymbols == null) {
                throw new MathException("Unrecognized symbols in propensity function " + prob + ". Propensity function should contain stochastic variable symbols only.");
            }
            if (symbols != null && varSymbols != null) {
                PropensitySolver.PropensityFunction pf = PropensitySolver.solvePropensity(prob, varSymbols, maxOrder);
                // get total order and save each var's order according to each reaction.
                for (int j = 0; j < pf.getSpeciesOrders().length; j++) {
                    varInProbOrderHash[i].put(pf.getSpeceisNames()[j], pf.getSpeciesOrders()[j]);
                    totalOrder = totalOrder + pf.getSpeciesOrders()[j];
                }
                // get rate constant
                coefExp = new Expression(pf.getRateExpression());
            }
        } else {
            coefExp = new Expression(prob);
        }
        if (totalOrder == 0) {
            results[i].setLawType(ReactionRateLaw.order_0);
            coefExp = new Expression(coefExp.flatten().infix() + "/6.02214179e23");
            try {
                coefExp.bindExpression(simSymbolTable);
                coefExp = simSymbolTable.substituteFunctions(coefExp).flatten();
                double val = coefExp.evaluateConstant();
                results[i].setRateConstant(val);
            } catch (Exception e) {
                e.printStackTrace(System.err);
                throw new ExpressionException(e.getMessage());
            }
        } else if (totalOrder == 1) {
            results[i].setLawType(ReactionRateLaw.order_1);
            coefExp = coefExp.flatten();
            try {
                coefExp.bindExpression(simSymbolTable);
                coefExp = simSymbolTable.substituteFunctions(coefExp).flatten();
                double val = coefExp.evaluateConstant();
                results[i].setRateConstant(val);
            } catch (Exception e) {
                e.printStackTrace(System.err);
                throw new ExpressionException(e.getMessage());
            }
        } else if (totalOrder == 2) {
            if (// second order, two same molecules
            varSymbols.length == 1) {
                // k= c*6.02214179e23/2, since in VCell, "/2" is already incorporated into c, so we don'y need to take care of this item from the conversion.
                coefExp = new Expression(coefExp.flatten().infix() + "*6.02214179e23");
                results[i].setLawType(ReactionRateLaw.order_2_1substrate);
                try {
                    coefExp.bindExpression(simSymbolTable);
                    coefExp = simSymbolTable.substituteFunctions(coefExp).flatten();
                    double val = coefExp.evaluateConstant();
                    results[i].setRateConstant(val);
                } catch (Exception e) {
                    e.printStackTrace(System.err);
                    throw new ExpressionException(e.getMessage());
                }
            } else if (// second order, two different molecules
            varSymbols.length == 2) {
                coefExp = new Expression(coefExp.flatten().infix() + "*6.02214179e23");
                results[i].setLawType(ReactionRateLaw.order_2_2substrate);
                try {
                    coefExp.bindExpression(simSymbolTable);
                    coefExp = simSymbolTable.substituteFunctions(coefExp).flatten();
                    double val = coefExp.evaluateConstant();
                    results[i].setRateConstant(val);
                } catch (Exception e) {
                    e.printStackTrace(System.err);
                    throw new ExpressionException(e.getMessage());
                }
            }
        } else if (totalOrder == 3) {
            if (// third order, three same molecules
            varSymbols.length == 1) {
                results[i].setLawType(ReactionRateLaw.order_3_1substrate);
                // use c directly.  "/3!" is already incorporated into c, so we compensate this item from the conversion.
                coefExp = new Expression(coefExp.flatten().infix() + "*6");
            } else if (// third order, three different molecules
            varSymbols.length == 3) {
                results[i].setLawType(ReactionRateLaw.order_3_3substrate);
            } else if (// third order, two different molecules
            varSymbols.length == 2) {
                results[i].setLawType(ReactionRateLaw.order_3_2substrate);
                // use c directly.  "/(2!*1!)" is already incorporated into c, so we compensate this item from the conversion.
                coefExp = new Expression(coefExp.flatten().infix() + "*2");
            }
            coefExp = coefExp.flatten();
            try {
                coefExp.bindExpression(simSymbolTable);
                coefExp = simSymbolTable.substituteFunctions(coefExp).flatten();
                double val = coefExp.evaluateConstant();
                results[i].setRateConstant(val);
            } catch (Exception e) {
                e.printStackTrace(System.err);
                throw new ExpressionException(e.getMessage());
            }
        } else // order more than 3, throw exception
        {
            throw new RuntimeException("Reaction order is more than 3, we couldn't solve it by Hybrid simulation.");
        }
    }
    return results;
}

Example 29 with MathException

use of cbit.vcell.math.MathException 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));
    }
}

Example 30 with MathException

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

the class ClientDocumentManager method substituteFieldFuncNames.

public void substituteFieldFuncNames(VCDocument vcDocument, VersionableTypeVersion originalOwner) throws DataAccessException, MathException, ExpressionException {
    Vector<ExternalDataIdentifier> errorCleanupExtDataIDV = new Vector<ExternalDataIdentifier>();
    try {
        if (originalOwner == null || originalOwner.getVersion().getOwner().compareEqual(getUser())) {
            // Substitution for FieldFunc not needed for new doc or if we own doc
            return;
        }
        // Get Objects from Document that might need to have FieldFuncs replaced
        Vector<Object> fieldFunctionContainer_mathDesc_or_simContextV = new Vector<Object>();
        if (vcDocument instanceof MathModel) {
            fieldFunctionContainer_mathDesc_or_simContextV.add(((MathModel) vcDocument).getMathDescription());
        } else if (vcDocument instanceof BioModel) {
            SimulationContext[] simContextArr = ((BioModel) vcDocument).getSimulationContexts();
            for (int i = 0; i < simContextArr.length; i += 1) {
                fieldFunctionContainer_mathDesc_or_simContextV.add(simContextArr[i]);
            }
        }
        // Get original Field names
        Vector<String> origFieldFuncNamesV = new Vector<String>();
        for (int i = 0; i < fieldFunctionContainer_mathDesc_or_simContextV.size(); i += 1) {
            Object fieldFunctionContainer = fieldFunctionContainer_mathDesc_or_simContextV.elementAt(i);
            FieldFunctionArguments[] fieldFuncArgsArr = null;
            if (fieldFunctionContainer instanceof MathDescription) {
                fieldFuncArgsArr = FieldUtilities.getFieldFunctionArguments((MathDescription) fieldFunctionContainer);
            } else if (fieldFunctionContainer instanceof SimulationContext) {
                fieldFuncArgsArr = ((SimulationContext) fieldFunctionContainer).getFieldFunctionArguments();
            }
            for (int j = 0; j < fieldFuncArgsArr.length; j += 1) {
                if (!origFieldFuncNamesV.contains(fieldFuncArgsArr[j].getFieldName())) {
                    origFieldFuncNamesV.add(fieldFuncArgsArr[j].getFieldName());
                }
            }
        }
        if (origFieldFuncNamesV.size() == 0) {
            // No FieldFunctions to substitute
            return;
        }
        FieldDataDBOperationResults copyNamesFieldDataOpResults = fieldDataDBOperation(FieldDataDBOperationSpec.createCopyNoConflictExtDataIDsSpec(getUser(), origFieldFuncNamesV.toArray(new String[0]), originalOwner));
        errorCleanupExtDataIDV.addAll(copyNamesFieldDataOpResults.oldNameNewIDHash.values());
        // Copy Field Data on Data Server FileSystem
        for (String fieldname : origFieldFuncNamesV) {
            KeyValue sourceSimDataKey = copyNamesFieldDataOpResults.oldNameOldExtDataIDKeyHash.get(fieldname);
            if (sourceSimDataKey == null) {
                throw new DataAccessException("Couldn't find original data key for FieldFunc " + fieldname);
            }
            ExternalDataIdentifier newExtDataID = copyNamesFieldDataOpResults.oldNameNewIDHash.get(fieldname);
            getSessionManager().fieldDataFileOperation(FieldDataFileOperationSpec.createCopySimFieldDataFileOperationSpec(newExtDataID, sourceSimDataKey, originalOwner.getVersion().getOwner(), FieldDataFileOperationSpec.JOBINDEX_DEFAULT, getUser()));
        }
        // Finally substitute new Field names
        for (int i = 0; i < fieldFunctionContainer_mathDesc_or_simContextV.size(); i += 1) {
            Object fieldFunctionContainer = fieldFunctionContainer_mathDesc_or_simContextV.elementAt(i);
            if (fieldFunctionContainer instanceof MathDescription) {
                MathDescription mathDesc = (MathDescription) fieldFunctionContainer;
                FieldUtilities.substituteFieldFuncNames(mathDesc, copyNamesFieldDataOpResults.oldNameNewIDHash);
            } else if (fieldFunctionContainer instanceof SimulationContext) {
                SimulationContext simContext = (SimulationContext) fieldFunctionContainer;
                simContext.substituteFieldFuncNames(copyNamesFieldDataOpResults.oldNameNewIDHash);
            }
        }
        fireFieldDataDB(new FieldDataDBEvent(this));
    } catch (Exception e) {
        e.printStackTrace();
        // Cleanup
        for (int i = 0; i < errorCleanupExtDataIDV.size(); i += 1) {
            try {
                fieldDataDBOperation(FieldDataDBOperationSpec.createDeleteExtDataIDSpec(errorCleanupExtDataIDV.elementAt(i)));
            } catch (Exception e2) {
            // ignore, we tried to cleanup
            }
            try {
                fieldDataFileOperation(FieldDataFileOperationSpec.createDeleteFieldDataFileOperationSpec(errorCleanupExtDataIDV.elementAt(i)));
            } catch (Exception e1) {
            // ignore, we tried to cleanup
            }
        }
        throw new RuntimeException("Error copying Field Data \n" + e.getMessage());
    }
}