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

Example 6 with ExpressionException

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

the class NFsimXMLWriter method getListOfFunctions.

private static Element getListOfFunctions(MathDescription mathDesc, SimulationSymbolTable simulationSymbolTable) throws SolverException {
    Element listOfParametersElement = new Element("ListOfFunctions");
    for (Variable var : simulationSymbolTable.getVariables()) {
        Double value = null;
        if (var instanceof Constant || var instanceof Function) {
            Expression valExpression = var.getExpression();
            Expression substitutedValExpr = null;
            try {
                substitutedValExpr = simulationSymbolTable.substituteFunctions(valExpression);
            } catch (Exception e) {
                e.printStackTrace(System.out);
                throw new SolverException("Constant or Function " + var.getName() + " substitution failed : exp = \"" + var.getExpression().infix() + "\": " + e.getMessage());
            }
            try {
                value = substitutedValExpr.evaluateConstant();
            } catch (ExpressionException e) {
                System.out.println("constant or function " + var.getName() + " = " + substitutedValExpr.infix() + " does not have a constant value");
            }
            Element functionElement = new Element("Function");
            functionElement.setAttribute("id", var.getName());
            if (value != null) {
                // parameter, see getListOfParameters() above
                continue;
            } else {
                Element listOfReferencesElement = new Element("ListOfReferences");
                String[] references = valExpression.getSymbols();
                for (int i = 0; i < references.length; i++) {
                    String reference = references[i];
                    Element referenceElement = new Element("Reference");
                    referenceElement.setAttribute("name", reference);
                    Variable referenceVariable = simulationSymbolTable.getVariable(reference);
                    Double referenceValue = null;
                    Expression referenceExpression = referenceVariable.getExpression();
                    Expression substitutedReferenceExpression = null;
                    if (referenceExpression != null) {
                        try {
                            substitutedReferenceExpression = simulationSymbolTable.substituteFunctions(referenceExpression);
                        } catch (Exception e) {
                            e.printStackTrace(System.out);
                            throw new SolverException("Constant or Function " + var.getName() + " substitution failed : exp = \"" + var.getExpression().infix() + "\": " + e.getMessage());
                        }
                        try {
                            referenceValue = substitutedReferenceExpression.evaluateConstant();
                        } catch (ExpressionException e) {
                            System.out.println("constant or function " + var.getName() + " = " + substitutedValExpr.infix() + " does not have a constant value");
                        }
                    }
                    if (referenceVariable instanceof ParticleObservable) {
                        referenceElement.setAttribute("type", "Observable");
                    } else if (referenceVariable instanceof Function) {
                        if (referenceValue != null) {
                            referenceElement.setAttribute("type", "ConstantExpression");
                        } else {
                            referenceElement.setAttribute("type", "Function");
                        }
                    } else {
                        // constant
                        referenceElement.setAttribute("type", "ConstantExpression");
                    }
                    listOfReferencesElement.addContent(referenceElement);
                }
                functionElement.addContent(listOfReferencesElement);
                Element expressionElement = new Element("Expression");
                String functionExpression = valExpression.infix();
                expressionElement.setText(functionExpression);
                functionElement.addContent(expressionElement);
            }
            listOfParametersElement.addContent(functionElement);
        }
    }
    return listOfParametersElement;
}

Example 7 with ExpressionException

use of cbit.vcell.parser.ExpressionException 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.DefaultMaxMoleculesPerSpecies;
            }
            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 8 with ExpressionException

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

the class NFsimXMLWriter method getListOfParameters.

private static Element getListOfParameters(MathDescription mathDesc, SimulationSymbolTable simulationSymbolTable) throws SolverException {
    Element listOfParametersElement = new Element("ListOfParameters");
    for (Variable var : simulationSymbolTable.getVariables()) {
        Double value = null;
        if (var instanceof Constant || var instanceof Function) {
            Expression valExpression = var.getExpression();
            Expression substitutedValExpr = null;
            try {
                substitutedValExpr = simulationSymbolTable.substituteFunctions(valExpression);
            } catch (Exception e) {
                e.printStackTrace(System.out);
                throw new SolverException("Constant or Function " + var.getName() + " substitution failed : exp = \"" + var.getExpression().infix() + "\": " + e.getMessage());
            }
            try {
                value = substitutedValExpr.evaluateConstant();
            } catch (ExpressionException e) {
                System.out.println("constant or function " + var.getName() + " = " + substitutedValExpr.infix() + " does not have a constant value");
            }
            Element parameterElement = new Element("Parameter");
            parameterElement.setAttribute("id", var.getName());
            if (value != null) {
                parameterElement.setAttribute("type", "Constant");
                parameterElement.setAttribute("value", value.toString());
            } else {
                // function, see getListOfFunctions() below
                continue;
            }
            listOfParametersElement.addContent(parameterElement);
        }
    }
    return listOfParametersElement;
}

Example 9 with ExpressionException

use of cbit.vcell.parser.ExpressionException 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 10 with ExpressionException

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

the class SmoldynFileWriter method writeDrifts.

private void writeDrifts() throws ExpressionBindingException, ExpressionException, MathException {
    // writer diffusion properties
    printWriter.println("# drift properties");
    Enumeration<SubDomain> subDomainEnumeration = mathDesc.getSubDomains();
    while (subDomainEnumeration.hasMoreElements()) {
        SubDomain subDomain = subDomainEnumeration.nextElement();
        List<ParticleProperties> particlePropertiesList = subDomain.getParticleProperties();
        for (ParticleProperties pp : particlePropertiesList) {
            String variableName = null;
            if (subDomain instanceof MembraneSubDomain) {
                variableName = getVariableName(pp.getVariable(), subDomain);
            } else {
                variableName = getVariableName(pp.getVariable(), null);
            }
            try {
                double driftX = 0.0;
                if (pp.getDriftX() != null) {
                    driftX = subsituteFlattenToConstant(pp.getDriftX());
                }
                double driftY = 0.0;
                if (pp.getDriftY() != null) {
                    driftY = subsituteFlattenToConstant(pp.getDriftY());
                }
                double driftZ = 0.0;
                if (pp.getDriftZ() != null) {
                    driftZ = subsituteFlattenToConstant(pp.getDriftZ());
                }
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.drift + " " + variableName + " " + driftX + " " + driftY + " " + driftZ);
            } catch (NotAConstantException ex) {
                throw new ExpressionException("diffusion coefficient for variable " + variableName + " is not a constant. Constants are required for all diffusion coefficients");
            }
        }
    }
    printWriter.println();
}