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

Example 21 with MathException

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

the class NFsimXMLWriter method getListOfSpecies.

private static Element getListOfSpecies(MathDescription mathDesc, SimulationSymbolTable simulationSymbolTable) throws SolverException {
    CompartmentSubDomain compartmentSubDomain = (CompartmentSubDomain) mathDesc.getSubDomains().nextElement();
    // 
    // NFsim expects a list of seed species.  These are concrete species patterns that have a "ParticleProperties" element defined (for initial conditions).
    // 
    Element listOfSpeciesElement = new Element("ListOfSpecies");
    for (int speciesIndex = 0; speciesIndex < compartmentSubDomain.getParticleProperties().size(); speciesIndex++) {
        // seedSpecies.getSpeciesPattern().resolveBonds();
        ParticleProperties particleProperties = compartmentSubDomain.getParticleProperties().get(speciesIndex);
        Element speciesElement = new Element("Species");
        String speciesID = "S" + (speciesIndex + 1);
        ParticleSpeciesPattern seedSpecies = (ParticleSpeciesPattern) particleProperties.getVariable();
        speciesElement.setAttribute("id", speciesID);
        speciesElement.setAttribute("name", seedSpecies.getName());
        List<ParticleInitialCondition> particleInitialConditions = particleProperties.getParticleInitialConditions();
        if (particleInitialConditions.size() != 1) {
            throw new SolverException("multiple particle initial conditions not expected for " + ParticleSpeciesPattern.class.getSimpleName() + " " + seedSpecies.getName());
        }
        // the initial conditions must be a count in math (ParticleInitialConditionCount)
        if (!(particleInitialConditions.get(0) instanceof ParticleInitialConditionCount)) {
            throw new SolverException("expecting initial count for " + ParticleSpeciesPattern.class.getSimpleName() + " " + seedSpecies.getName());
        }
        ParticleInitialConditionCount initialCount = (ParticleInitialConditionCount) particleInitialConditions.get(0);
        try {
            double value = evaluateConstant(initialCount.getCount(), simulationSymbolTable);
            Integer maxMoleculesPerType = simulationSymbolTable.getSimulation().getSolverTaskDescription().getNFSimSimulationOptions().getMaxMoleculesPerType();
            if (maxMoleculesPerType == null) {
                maxMoleculesPerType = NFsimSimulationOptions.DefaultMaxMoleculesPerType;
            }
            if (maxMoleculesPerType.doubleValue() < value) {
                String eMessage = "The Initial count for Species '" + seedSpecies.getName() + "' is " + BigDecimal.valueOf(value).toBigInteger();
                eMessage += ", which is higher than the limit of " + maxMoleculesPerType + ".\n";
                eMessage += "Please do one of the following: \n- reduce the Initial Condition value for this Species or reduce the compartment size\n";
                eMessage += "- increase the maximal number of Molecules per Molecular Type in the Advanced Solver Options panel.";
                throw new RuntimeException(eMessage);
            }
            speciesElement.setAttribute("concentration", Double.toString(value));
        } catch (ExpressionException | MathException e) {
            e.printStackTrace();
            throw new SolverException("error processing initial count of " + ParticleSpeciesPattern.class.getSimpleName() + " " + seedSpecies.getName() + ": " + e.getMessage());
        }
        HashMap<Bond, BondSites> bondSiteMapping = new HashMap<Bond, BondSites>();
        Element listOfMoleculesElement = getListOfMolecules(speciesID, seedSpecies, bondSiteMapping);
        speciesElement.addContent(listOfMoleculesElement);
        if (bondSiteMapping.size() > 0) {
            Element listOfBondsElement = getListOfBonds(bondSiteMapping);
            speciesElement.addContent(listOfBondsElement);
        }
        listOfSpeciesElement.addContent(speciesElement);
    }
    return listOfSpeciesElement;
}

Example 22 with MathException

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

the class SmoldynFileWriter method writeMolecules.

private void writeMolecules() throws ExpressionException, MathException {
    // write molecules
    StringBuilder sb = new StringBuilder();
    int max_mol = 0;
    Enumeration<SubDomain> subDomainEnumeration = mathDesc.getSubDomains();
    while (subDomainEnumeration.hasMoreElements()) {
        SubDomain subDomain = subDomainEnumeration.nextElement();
        for (ParticleProperties particleProperties : subDomain.getParticleProperties()) {
            ArrayList<ParticleInitialCondition> particleInitialConditions = particleProperties.getParticleInitialConditions();
            String variableName = getVariableName(particleProperties.getVariable(), subDomain);
            for (ParticleInitialCondition pic : particleInitialConditions) {
                if (pic instanceof ParticleInitialConditionCount) {
                    max_mol += writeInitialCount((ParticleInitialConditionCount) pic, subDomain, variableName, sb);
                } else if (pic instanceof ParticleInitialConditionConcentration) {
                    max_mol += writeInitialConcentration((ParticleInitialConditionConcentration) pic, subDomain, particleProperties.getVariable(), variableName, sb);
                }
            }
            if (lg.isDebugEnabled()) {
                lg.debug("subdomain " + subDomain.getName() + ' ' + variableName + " processed, maximum mol estimate now " + max_mol);
            }
        }
    }
    if (max_mol > MAX_MOLECULE_LIMIT) {
        throw new MathException(VCellErrorMessages.getSmoldynMaxMolReachedErrorMessage((long) max_mol, MAX_MOLECULE_LIMIT));
    }
    int max_adjusted = max_mol * MOLECULE_MAX_COEFFICIENT;
    if (max_adjusted < MIN_MOLECULE_LIMIT) {
        if (lg.isInfoEnabled()) {
            lg.info("adjusting computed max " + max_adjusted + " to minimum " + MIN_MOLECULE_LIMIT);
        }
        max_adjusted = MIN_MOLECULE_LIMIT;
    }
    if (max_adjusted > MAX_MOLECULE_LIMIT) {
        if (lg.isInfoEnabled()) {
            lg.info("adjusting computed max " + max_adjusted + " to maximum " + MAX_MOLECULE_LIMIT);
        }
        max_adjusted = MAX_MOLECULE_LIMIT;
    }
    printWriter.println("# molecules");
    printWriter.println(SmoldynVCellMapper.SmoldynKeyword.max_mol + " " + max_adjusted);
    printWriter.println(sb);
}

Example 23 with MathException

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

the class SmoldynFileWriter method writeReactions.

private void writeReactions() throws ExpressionException, MathException {
    printWriter.println("# reactions");
    Enumeration<SubDomain> subdomains = mathDesc.getSubDomains();
    while (subdomains.hasMoreElements()) {
        SubDomain subdomain = subdomains.nextElement();
        for (ParticleJumpProcess pjp : subdomain.getParticleJumpProcesses()) {
            ArrayList<Variable> reactants = new ArrayList<Variable>();
            ArrayList<Variable> products = new ArrayList<Variable>();
            for (Action a : pjp.getActions().toArray(new Action[pjp.getActions().size()])) {
                if (a.getOperation().equals(Action.ACTION_CREATE)) {
                    products.add(a.getVar());
                } else if (a.getOperation().equals(Action.ACTION_DESTROY)) {
                    reactants.add(a.getVar());
                }
            }
            Expression rateDefinition = null;
            JumpProcessRateDefinition jprd = pjp.getParticleRateDefinition();
            if (jprd instanceof MacroscopicRateConstant) {
                rateDefinition = subsituteFlatten(((MacroscopicRateConstant) jprd).getExpression());
            } else if (jprd instanceof InteractionRadius) {
                rateDefinition = subsituteFlatten(((InteractionRadius) jprd).getExpression());
            } else {
                new RuntimeException("The jump process rate definition is not supported");
            }
            if (rateDefinition.isZero()) {
                continue;
            }
            if (mathDesc.isSpatialHybrid()) {
                String[] symbols = rateDefinition.getSymbols();
                if (symbols != null) {
                    if (subdomain instanceof MembraneSubDomain) {
                        rateDefinition = new Expression(FiniteVolumeFileWriter.replaceVolumeVariable(getSimulationTask(), (MembraneSubDomain) subdomain, rateDefinition));
                    }
                }
            } else {
                try {
                    rateDefinition.evaluateConstant();
                } catch (ExpressionException ex) {
                    throw new ExpressionException("reaction rate for jump process " + pjp.getName() + " is not a constant. Constants are required for all reaction rates.");
                }
            }
            // Smoldyn takes maximum 2nd order reaction.
            if (reactants.size() > 2) {
                throw new MathException("VCell spatial stochastic models support up to 2nd order reactions. \n" + "The reaction:" + pjp.getName() + " has more than 2 reactants.");
            }
            if (products.size() > 2) {
                throw new MathException("VCell spatial stochastic models support up to 2nd order reactions. \n" + "The reaction:" + pjp.getName() + " has more than 2 products.");
            }
            String rateDefinitionStr = simulation.getMathDescription().isSpatialHybrid() ? rateDefinition.infix() + ";" : rateDefinition.evaluateConstant() + "";
            if (subdomain instanceof CompartmentSubDomain) {
                // 0th order reaction, product limited to one and we'll let the reaction know where it happens
                if (reactants.size() == 0 && products.size() == 1) {
                    printWriter.print(SmoldynVCellMapper.SmoldynKeyword.reaction_cmpt + " " + subdomain.getName() + " " + pjp.getName() + " ");
                } else {
                    printWriter.print(SmoldynVCellMapper.SmoldynKeyword.reaction + " " + /* + subdomain.getName() + " "*/
                    pjp.getName() + " ");
                }
                writeReactionCommand(reactants, products, subdomain, rateDefinitionStr);
            } else if (subdomain instanceof MembraneSubDomain) {
                // 0th order reaction, product limited to one and it can be on mem or in vol
                if (reactants.size() == 0 && products.size() == 1) {
                    printWriter.print(SmoldynVCellMapper.SmoldynKeyword.reaction_surface + " " + subdomain.getName() + " " + pjp.getName() + " ");
                    writeReactionCommand(reactants, products, subdomain, rateDefinitionStr);
                } else // consuming of a species to nothing, limited to one reactant
                if (reactants.size() == 1 && products.size() == 0) {
                    if (// consuming a mem species in mem reaction
                    getMembraneVariableCount(reactants) == 1) {
                        printWriter.print(SmoldynVCellMapper.SmoldynKeyword.reaction_surface + " " + subdomain.getName() + " " + pjp.getName() + " ");
                        writeReactionCommand(reactants, products, subdomain, rateDefinitionStr);
                    } else // it equals to adsorption, species A from vol adsorbed to mem as again species A, and then we kill the speceis A on mem.
                    if (getVolumeVariableCount(reactants) == 1) {
                        writeRateTransitionCommand(reactants, products, subdomain, rateDefinitionStr);
                        String speciesName = reactants.get(0).getName();
                        String killMolCmd = "cmd " + SmoldynVCellMapper.SmoldynKeyword.E + " " + SmoldynVCellMapper.SmoldynKeyword.killmol + " " + speciesName + "(" + SmoldynKeyword.up + ")";
                        killMolCommands.add(killMolCmd);
                    }
                } else // Use rate command for any membrane reactions with 1 reactant and 1 product
                if ((reactants.size() == 1) && (products.size() == 1)) {
                    // Membrane reaction (1 react to 1 product).
                    if (getMembraneVariableCount(products) == 1 && getMembraneVariableCount(reactants) == 1) {
                        printWriter.print(SmoldynVCellMapper.SmoldynKeyword.reaction_surface + " " + subdomain.getName() + " " + pjp.getName() + " ");
                        writeReactionCommand(reactants, products, subdomain, rateDefinitionStr);
                    } else // Other single molecular reactions
                    {
                        writeRateTransitionCommand(reactants, products, subdomain, rateDefinitionStr);
                    }
                } else // membrane reactions which are not one to one, or 0th order, or consuming species
                {
                    if (// membrane reaction has one membrane bound reactant
                    (getMembraneVariableCount(reactants) == 1)) {
                        printWriter.print(SmoldynVCellMapper.SmoldynKeyword.reaction_surface + " " + subdomain.getName() + " " + pjp.getName() + " ");
                        writeReactionCommand(reactants, products, subdomain, rateDefinitionStr);
                    } else if (// bimolecular membrane reaction
                    getMembraneVariableCount(reactants) == 2) {
                        if (jprd instanceof InteractionRadius) {
                            printWriter.print(SmoldynVCellMapper.SmoldynKeyword.reaction_surface + " " + subdomain.getName() + " " + pjp.getName() + " ");
                            writeReactionByInteractionRadius(reactants, products, subdomain, rateDefinitionStr, pjp.getName());
                        } else {
                            // throw new MathException("Error with reaction: " + pjp.getName() + ".\nVCell Spatial stochastic modeling requires macroscopic or microscopic kinetics for bimolecular membrane reactions.");
                            printWriter.print(SmoldynVCellMapper.SmoldynKeyword.reaction_surface + " " + subdomain.getName() + " " + pjp.getName() + " ");
                            writeReactionCommand(reactants, products, subdomain, rateDefinitionStr);
                        }
                    } else if (getMembraneVariableCount(reactants) == 0) {
                        throw new MathException("Error with reaction: " + pjp.getName() + ".\nIn VCell spatial stochastic modeling, the membrane reaction requires at least one membrane bound reactant.");
                    }
                }
            }
        }
    }
    printWriter.println();
}

Example 24 with MathException

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

the class SmoldynSolver method initialize.

/**
 *  This method takes the place of the old runUnsteady()...
 */
protected void initialize() throws SolverException {
    if (lg.isTraceEnabled())
        lg.trace("SmoldynSolver.initialize()");
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INIT);
    writeFunctionsFile();
    // write subdomains file
    try {
        SubdomainInfo.write(new File(getBaseName() + SimDataConstants.SUBDOMAINS_FILE_SUFFIX), simTask.getSimulation().getMathDescription());
    } catch (IOException e1) {
        e1.printStackTrace();
        throw new SolverException(e1.getMessage());
    } catch (MathException e1) {
        e1.printStackTrace();
        throw new SolverException(e1.getMessage());
    }
    String inputFilename = getInputFilename();
    if (lg.isTraceEnabled())
        lg.trace("SmoldynSolver.initialize() baseName = " + getBaseName());
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_INPUT_FILE));
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INPUT_FILE);
    PrintWriter pw = null;
    try {
        pw = new PrintWriter(inputFilename);
        if (SystemUtils.IS_OS_WINDOWS) {
            // 
            // the windows executable is compiled under cygwin (or mingw) and expect Unix style line termination characters.
            // so SmoldynInput file is written with platform default Java convention (different on windows) to a String.
            // Then the string is translated to Unix style before written to the file.
            // smoldyn is particularly sensitive to this issue, other compiled solvers are more tolerant.
            // 
            StringWriter stringWriter = new StringWriter();
            PrintWriter pw2 = new PrintWriter(stringWriter);
            SmoldynFileWriter stFileWriter = new SmoldynFileWriter(pw2, false, getBaseName(), simTask, bMessaging);
            stFileWriter.write();
            String fileContents = stringWriter.getBuffer().toString();
            fileContents = fileContents.replace("\r\n", "\n");
            pw.write(fileContents);
        } else {
            // 
            // for linux or macos, no translation is necessary.
            // 
            SmoldynFileWriter stFileWriter = new SmoldynFileWriter(pw, false, getBaseName(), simTask, bMessaging);
            stFileWriter.write();
        }
    } catch (Exception e) {
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_ABORTED, SimulationMessage.solverAborted("Could not generate input file: " + e.getMessage())));
        e.printStackTrace(System.out);
        throw new SolverException(e.getMessage());
    } finally {
        if (pw != null) {
            pw.close();
        }
    }
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_START));
    // get executable path+name.
    setMathExecutable(new MathExecutable(getMathExecutableCommand(), getSaveDirectory()));
// setMathExecutable(new cbit.vcell.solvers.MathExecutable(executableName + " gibson " + getBaseName() + ".stochInput" + " " + getBaseName() + ".stoch"));
}

Example 25 with MathException

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

the class ModelOptimizationMapping method getRemappedReferenceData.

/**
 * Gets the constraintData property (cbit.vcell.opt.ConstraintData) value.
 * @return The constraintData property value.
 * @see #setConstraintData
 */
private ReferenceData getRemappedReferenceData(MathMapping mathMapping) throws MappingException {
    if (modelOptimizationSpec.getReferenceData() == null) {
        return null;
    }
    // 
    // make sure time is mapped
    // 
    ReferenceData refData = modelOptimizationSpec.getReferenceData();
    ReferenceDataMappingSpec[] refDataMappingSpecs = modelOptimizationSpec.getReferenceDataMappingSpecs();
    RowColumnResultSet rowColResultSet = new RowColumnResultSet();
    Vector<SymbolTableEntry> modelObjectList = new Vector<SymbolTableEntry>();
    Vector<double[]> dataList = new Vector<double[]>();
    // 
    // find bound columns, (time is always mapped to the first column)
    // 
    int mappedColumnCount = 0;
    for (int i = 0; i < refDataMappingSpecs.length; i++) {
        SymbolTableEntry modelObject = refDataMappingSpecs[i].getModelObject();
        if (modelObject != null) {
            int mappedColumnIndex = mappedColumnCount;
            if (modelObject instanceof Model.ReservedSymbol && ((ReservedSymbol) modelObject).isTime()) {
                mappedColumnIndex = 0;
            }
            String origRefDataColumnName = refDataMappingSpecs[i].getReferenceDataColumnName();
            int origRefDataColumnIndex = refData.findColumn(origRefDataColumnName);
            if (origRefDataColumnIndex < 0) {
                throw new RuntimeException("reference data column named '" + origRefDataColumnName + "' not found");
            }
            double[] columnData = refData.getDataByColumn(origRefDataColumnIndex);
            if (modelObjectList.contains(modelObject)) {
                throw new RuntimeException("multiple reference data columns mapped to same model object '" + modelObject.getName() + "'");
            }
            modelObjectList.insertElementAt(modelObject, mappedColumnIndex);
            dataList.insertElementAt(columnData, mappedColumnIndex);
            mappedColumnCount++;
        }
    }
    // 
    if (modelObjectList.size() == 0) {
        throw new RuntimeException("reference data was not associated with model");
    }
    if (modelObjectList.size() == 1) {
        throw new RuntimeException("reference data was not associated with model, must map time and at least one other column");
    }
    boolean bFoundTimeVar = false;
    for (SymbolTableEntry ste : modelObjectList) {
        if (ste instanceof Model.ReservedSymbol && ((ReservedSymbol) ste).isTime()) {
            bFoundTimeVar = true;
            break;
        }
    }
    if (!bFoundTimeVar) {
        throw new RuntimeException("must map time column of reference data to model");
    }
    // 
    for (int i = 0; i < modelObjectList.size(); i++) {
        SymbolTableEntry modelObject = (SymbolTableEntry) modelObjectList.elementAt(i);
        try {
            // Find by name because MathSybolMapping has different 'objects' than refDataMapping 'objects'
            Variable variable = mathMapping.getMathSymbolMapping().findVariableByName(modelObject.getName());
            if (variable != null) {
                String symbol = variable.getName();
                rowColResultSet.addDataColumn(new ODESolverResultSetColumnDescription(symbol));
            } else if (modelObject instanceof Model.ReservedSymbol && ((Model.ReservedSymbol) modelObject).isTime()) {
                Model.ReservedSymbol time = (Model.ReservedSymbol) modelObject;
                String symbol = time.getName();
                rowColResultSet.addDataColumn(new ODESolverResultSetColumnDescription(symbol));
            }
        } catch (MathException | MatrixException | ExpressionException | ModelException e) {
            e.printStackTrace();
            throw new MappingException(e.getMessage(), e);
        }
    }
    // 
    // populate data columns (time and rest)
    // 
    double[] weights = new double[rowColResultSet.getColumnDescriptionsCount()];
    weights[0] = 1.0;
    int numRows = ((double[]) dataList.elementAt(0)).length;
    int numColumns = modelObjectList.size();
    for (int j = 0; j < numRows; j++) {
        double[] row = new double[numColumns];
        for (int i = 0; i < numColumns; i++) {
            row[i] = ((double[]) dataList.elementAt(i))[j];
            if (i > 0) {
                weights[i] += row[i] * row[i];
            }
        }
        rowColResultSet.addRow(row);
    }
    for (int i = 0; i < numColumns; i++) {
        if (weights[i] == 0) {
            weights[i] = 1;
        } else {
            weights[i] = 1 / weights[i];
        }
    }
    SimpleReferenceData remappedRefData = new SimpleReferenceData(rowColResultSet, weights);
    return remappedRefData;
}