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

Example 16 with Equation

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

the class Jacobian method parseMathDesc.

/**
 * This method was created by a SmartGuide.
 * @exception java.lang.Exception The exception description.
 */
private void parseMathDesc() throws MathException {
    Vector equationList = new Vector();
    Enumeration enum1 = subDomain.getEquations();
    while (enum1.hasMoreElements()) {
        Equation equ = (Equation) enum1.nextElement();
        if (equ instanceof OdeEquation) {
            equationList.addElement(equ);
        } else {
            throw new MathException("encountered non-ode equation, unsupported");
        }
    }
    Vector variableList = new Vector();
    enum1 = mathDesc.getVariables();
    while (enum1.hasMoreElements()) {
        Variable var = (Variable) enum1.nextElement();
        if (var instanceof VolVariable) {
            variableList.addElement(var);
        }
    }
    if (equationList.size() != variableList.size()) {
        throw new MathException("there are " + equationList.size() + " equations and " + variableList.size() + " variables");
    }
    numVariables = variableList.size();
    rates = new Expression[numVariables];
    vars = new VolVariable[numVariables];
    for (int i = 0; i < numVariables; i++) {
        OdeEquation odeEqu = (OdeEquation) equationList.elementAt(i);
        rates[i] = odeEqu.getRateExpression();
        vars[i] = (VolVariable) odeEqu.getVariable();
    }
}

Example 17 with Equation

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

the class SundialsSolver method createStateVariables.

/*
	This method was created in Visual Age
*/
private StateVariable[] createStateVariables() throws MathException, ExpressionException {
    Vector<StateVariable> stateVariables = new Vector<StateVariable>();
    // get Ode's from MathDescription and create ODEStateVariables
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    MathDescription mathDescription = simSymbolTable.getSimulation().getMathDescription();
    Enumeration<Equation> enum1 = ((SubDomain) mathDescription.getSubDomains().nextElement()).getEquations();
    while (enum1.hasMoreElements()) {
        Equation equation = (Equation) enum1.nextElement();
        if (equation instanceof OdeEquation) {
            stateVariables.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>();
    if (getSensitivityParameter() != null) {
        for (int i = 0; i < variables.length; i++) {
            if (variables[i] instanceof VolVariable) {
                VolVariable volVariable = (VolVariable) variables[i];
                SensVariable sv = new SensVariable(volVariable, getSensitivityParameter());
                sensVariables.addElement(sv);
            }
        }
    }
    if (rateSensitivity == null) {
        rateSensitivity = new RateSensitivity(mathDescription, mathDescription.getSubDomains().nextElement());
    }
    if (jacobian == null) {
        jacobian = new Jacobian(mathDescription, mathDescription.getSubDomains().nextElement());
    }
    for (int v = 0; v < sensVariables.size(); v++) {
        stateVariables.addElement(new SensStateVariable((SensVariable) sensVariables.elementAt(v), rateSensitivity, jacobian, sensVariables, simSymbolTable));
    }
    if (stateVariables.size() == 0) {
        throw new MathException("there are no equations defined");
    }
    StateVariable[] stateVars = (StateVariable[]) BeanUtils.getArray(stateVariables, StateVariable.class);
    return (stateVars);
}

Example 18 with Equation

use of cbit.vcell.math.Equation 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 19 with Equation

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

the class MathTestingUtilities method constructOdesForSensitivity.

// 
// This method is used to solve for sensitivity of variables to a given parameter.
// The mathDescription and the sensitivity parameter are passed as arguments.
// New variables and ODEs are constructed according to the rule listed below and are added to the mathDescription.
// The method returns the modified mathDescription.
// 
public static MathDescription constructOdesForSensitivity(MathDescription mathDesc, Constant sensParam) throws ExpressionException, MathException, MappingException {
    // 
    // For each ODE :
    // 
    // dX/dt = F(X, P)
    // 
    // (where P is the sensitivity parameter)
    // 
    // we create two other ODEs :
    // 
    // dX_1/dt = F(X_1, P_1)    and
    // 
    // dX_2/dt = F(X_2, P_2)
    // 
    // where P_1 = P + epsilon, and
    // P_2 = P - epsilon.
    // 
    // We keep the initial conditions for both the new ODEs to be the same,
    // i.e., X_1_init = X_2_init.
    // 
    // Then, solving for X_1 & X_2, sensitivity of X wrt P can be computed as :
    // 
    // dX = (X_1 - X_2)
    // --	 -----------   .
    // dP	 (P_1 - P_2)
    // 
    // 
    // REMOVE PRINTS AFTER CHECKING !!!
    System.out.println(" \n\n------------  Old Math Description -----------------");
    System.out.println(mathDesc.getVCML_database());
    if (mathDesc.getGeometry().getDimension() > 0) {
        throw new RuntimeException("Suppport for Spatial systems not yet implemented.");
    }
    VariableHash varHash = new VariableHash();
    Enumeration<Variable> enumVar = mathDesc.getVariables();
    while (enumVar.hasMoreElements()) {
        varHash.addVariable(enumVar.nextElement());
    }
    // 
    // Get 2 values of senstivity parameter (P + epsilon) & (P - epsilon)
    // 
    Constant epsilon = new Constant("epsilon", new Expression(sensParam.getConstantValue() * 1e-3));
    Constant sensParam1 = new Constant(sensParam.getName() + "_1", new Expression(sensParam.getConstantValue() + epsilon.getConstantValue()));
    Constant sensParam2 = new Constant(sensParam.getName() + "_2", new Expression(sensParam.getConstantValue() - epsilon.getConstantValue()));
    // 
    // Iterate through each subdomain (only 1 in compartmental case), and each equation in the subdomain
    // 
    Enumeration<SubDomain> subDomainEnum = mathDesc.getSubDomains();
    // 
    // Create a vector of equations to store the 2 equations for each ODE variable in the subdomain.
    // Later, add it to the equations list in the subdomain.
    // 
    Vector<Equation> equnsVector = new Vector<Equation>();
    Vector<Variable> varsVector = new Vector<Variable>();
    Vector<Variable> var1s = new Vector<Variable>();
    Vector<Variable> var2s = new Vector<Variable>();
    while (subDomainEnum.hasMoreElements()) {
        SubDomain subDomain = subDomainEnum.nextElement();
        Enumeration<Equation> equationEnum = subDomain.getEquations();
        Domain domain = new Domain(subDomain);
        while (equationEnum.hasMoreElements()) {
            Equation equation = equationEnum.nextElement();
            if (equation instanceof OdeEquation) {
                OdeEquation odeEquation = (OdeEquation) equation;
                // Similar to substituteWithExactSolutions, to bind and substitute functions in the ODE
                Expression substitutedRateExp = substituteFunctions(odeEquation.getRateExpression(), mathDesc);
                String varName = odeEquation.getVariable().getName();
                VolVariable var = new VolVariable(varName, domain);
                varsVector.addElement(var);
                // 
                // Create the variable var1, and get the initExpr and rateExpr from the original ODE.
                // Substitute the new vars (var1 and param1) in the old initExpr and rateExpr and create a new ODE
                // 
                String varName1 = new String("__" + varName + "_1");
                Expression initExpr1 = odeEquation.getInitialExpression();
                Expression rateExpr1 = new Expression(substitutedRateExp);
                rateExpr1.substituteInPlace(new Expression(varName), new Expression(varName1));
                rateExpr1.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam1.getName()));
                VolVariable var1 = new VolVariable(varName1, domain);
                var1s.addElement(var1);
                OdeEquation odeEqun1 = new OdeEquation(var1, initExpr1, rateExpr1);
                equnsVector.addElement(odeEqun1);
                // 
                // Create the variable var2, and get the initExpr and rateExpr from the original ODE.
                // Substitute the new vars (var2 and param2) in the old initExpr and rateExpr and create a new ODE
                // 
                String varName2 = new String("__" + varName + "_2");
                Expression initExpr2 = odeEquation.getInitialExpression();
                Expression rateExpr2 = new Expression(substitutedRateExp);
                rateExpr2.substituteInPlace(new Expression(varName), new Expression(varName2));
                rateExpr2.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam2.getName()));
                VolVariable var2 = new VolVariable(varName2, domain);
                var2s.addElement(var2);
                OdeEquation odeEqun2 = new OdeEquation(var2, initExpr2, rateExpr2);
                equnsVector.addElement(odeEqun2);
                // 
                // Create a function for the sensitivity function expression (X1-X2)/(P1-P2), and save in varHash
                // 
                Expression diffVar = Expression.add(new Expression(var1.getName()), Expression.negate(new Expression(var2.getName())));
                Expression diffParam = Expression.add(new Expression(sensParam1.getName()), Expression.negate(new Expression(sensParam2.getName())));
                Expression sensitivityExpr = Expression.mult(diffVar, Expression.invert(diffParam));
                Function sens_Func = new Function("__sens" + varName + "_wrt_" + sensParam.getName(), sensitivityExpr, domain);
                varHash.addVariable(epsilon);
                varHash.addVariable(sensParam1);
                varHash.addVariable(sensParam2);
                varHash.addVariable(var1);
                varHash.addVariable(var2);
                varHash.addVariable(sens_Func);
            } else {
                // sensitivity not implemented for PDEs or other equation types.
                throw new RuntimeException("SolverTest.constructedExactMath(): equation type " + equation.getClass().getName() + " not yet implemented");
            }
        }
        // 
        // Need to substitute the new variables in the new ODEs.
        // i.e., if Rate Expr for ODE_1 for variable X_1 contains variable Y, variable Z, etc.
        // Rate Expr is already substituted with X_1, but it also needs substitute Y with Y_1, Z with Z_1, etc.
        // So get the volume variables, from the vectors for vars, var_1s and var_2s
        // Substitute the rate expressions for the newly added ODEs in equnsVector.
        // 
        Variable[] vars = (Variable[]) BeanUtils.getArray(varsVector, Variable.class);
        Variable[] var_1s = (Variable[]) BeanUtils.getArray(var1s, Variable.class);
        Variable[] var_2s = (Variable[]) BeanUtils.getArray(var2s, Variable.class);
        Vector<Equation> newEqunsVector = new Vector<Equation>();
        for (int i = 0; i < equnsVector.size(); i++) {
            Equation equn = equnsVector.elementAt(i);
            Expression initEx = equn.getInitialExpression();
            Expression rateEx = equn.getRateExpression();
            for (int j = 0; j < vars.length; j++) {
                if (equn.getVariable().getName().endsWith("_1")) {
                    rateEx.substituteInPlace(new Expression(vars[j].getName()), new Expression(var_1s[j].getName()));
                } else if (equn.getVariable().getName().endsWith("_2")) {
                    rateEx.substituteInPlace(new Expression(vars[j].getName()), new Expression(var_2s[j].getName()));
                }
            }
            OdeEquation odeEqun = new OdeEquation(equn.getVariable(), initEx, rateEx);
            newEqunsVector.addElement(odeEqun);
        }
        // 
        for (int i = 0; i < newEqunsVector.size(); i++) {
            mathDesc.getSubDomain(subDomain.getName()).addEquation((Equation) newEqunsVector.elementAt(i));
        }
        // 
        // FAST SYSTEM
        // If the subdomain has a fast system, create a new fast system by substituting the high-low variables/parameters
        // in the expressions for the fastInvariants and fastRates and adding them to the fast system.
        // 
        Vector<FastInvariant> invarsVector = new Vector<FastInvariant>();
        Vector<FastRate> ratesVector = new Vector<FastRate>();
        Enumeration<FastInvariant> fastInvarsEnum = null;
        Enumeration<FastRate> fastRatesEnum = null;
        // Get the fast invariants and fast rates in the system.
        FastSystem fastSystem = subDomain.getFastSystem();
        if (fastSystem != null) {
            fastInvarsEnum = fastSystem.getFastInvariants();
            fastRatesEnum = fastSystem.getFastRates();
            // 
            while (fastInvarsEnum.hasMoreElements()) {
                FastInvariant fastInvar = fastInvarsEnum.nextElement();
                Expression fastInvarExpr = fastInvar.getFunction();
                fastInvarExpr = MathUtilities.substituteFunctions(fastInvarExpr, mathDesc);
                Expression fastInvarExpr1 = new Expression(fastInvarExpr);
                Expression fastInvarExpr2 = new Expression(fastInvarExpr);
                for (int i = 0; i < vars.length; i++) {
                    fastInvarExpr1.substituteInPlace(new Expression(vars[i].getName()), new Expression(var_1s[i].getName()));
                    fastInvarExpr2.substituteInPlace(new Expression(vars[i].getName()), new Expression(var_2s[i].getName()));
                }
                fastInvarExpr1.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam1.getName()));
                FastInvariant fastInvar1 = new FastInvariant(fastInvarExpr1);
                invarsVector.addElement(fastInvar1);
                fastInvarExpr2.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam2.getName()));
                FastInvariant fastInvar2 = new FastInvariant(fastInvarExpr2);
                invarsVector.addElement(fastInvar2);
            }
            // Add the newly created fast invariants to the existing list of fast invariants in the fast system.
            for (int i = 0; i < invarsVector.size(); i++) {
                FastInvariant inVar = (FastInvariant) invarsVector.elementAt(i);
                fastSystem.addFastInvariant(inVar);
            }
            // 
            while (fastRatesEnum.hasMoreElements()) {
                FastRate fastRate = fastRatesEnum.nextElement();
                Expression fastRateExpr = fastRate.getFunction();
                fastRateExpr = MathUtilities.substituteFunctions(fastRateExpr, mathDesc);
                Expression fastRateExpr1 = new Expression(fastRateExpr);
                Expression fastRateExpr2 = new Expression(fastRateExpr);
                for (int i = 0; i < vars.length; i++) {
                    fastRateExpr1.substituteInPlace(new Expression(vars[i].getName()), new Expression(var_1s[i].getName()));
                    fastRateExpr2.substituteInPlace(new Expression(vars[i].getName()), new Expression(var_2s[i].getName()));
                }
                fastRateExpr1.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam1.getName()));
                FastRate fastRate1 = new FastRate(fastRateExpr1);
                ratesVector.addElement(fastRate1);
                fastRateExpr2.substituteInPlace(new Expression(sensParam.getName()), new Expression(sensParam2.getName()));
                FastRate fastRate2 = new FastRate(fastRateExpr2);
                ratesVector.addElement(fastRate2);
            }
            // Add the newly created fast rates to the existing list of fast rates in the fast system.
            for (int i = 0; i < ratesVector.size(); i++) {
                FastRate rate = (FastRate) ratesVector.elementAt(i);
                fastSystem.addFastRate(rate);
            }
        }
    }
    // Reset all variables in mathDesc.
    mathDesc.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
    // REMOVE PRINTS AFTER CHECKING
    System.out.println(" \n\n------------  New Math Description -----------------");
    System.out.println(mathDesc.getVCML_database());
    return mathDesc;
}

Example 20 with Equation

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

the class ConstructedSolutionTemplate method initialize.

/**
 * Insert the method's description here.
 * Creation date: (5/12/2003 11:04:13 AM)
 * @param mathDesc cbit.vcell.math.MathDescription
 */
private void initialize(cbit.vcell.math.MathDescription mathDesc) {
    // 
    // for all valid combinations of variables/domains ... add a solution template with a default solution.
    // 
    java.util.Vector solutionTemplateList = new java.util.Vector();
    Enumeration enumSubDomains = mathDesc.getSubDomains();
    while (enumSubDomains.hasMoreElements()) {
        SubDomain subDomain = (SubDomain) enumSubDomains.nextElement();
        Enumeration enumEquations = subDomain.getEquations();
        while (enumEquations.hasMoreElements()) {
            Equation equation = (Equation) enumEquations.nextElement();
            Variable var = equation.getVariable();
            String baseName = " " + var.getName() + "_" + subDomain.getName();
            String amplitudeName = baseName + "_A";
            String tau1Name = baseName + "_tau1";
            String tau2Name = baseName + "_tau2";
            if (equation instanceof OdeEquation) {
                try {
                    Expression exp = new Expression(amplitudeName + " * (1.0 + exp(-t/" + tau1Name + ")*sin(2*" + Math.PI + "/" + tau2Name + "*t))");
                    solutionTemplateList.add(new SolutionTemplate(equation.getVariable().getName(), subDomain.getName(), exp));
                } catch (cbit.vcell.parser.ExpressionException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException(e.getMessage());
                }
            } else if (equation instanceof PdeEquation) {
                try {
                    Expression exp = new Expression(amplitudeName + " * (1.0 + exp(-t/" + tau1Name + ") + " + tau2Name + "*x)");
                    solutionTemplateList.add(new SolutionTemplate(equation.getVariable().getName(), subDomain.getName(), exp));
                } catch (cbit.vcell.parser.ExpressionException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException(e.getMessage());
                }
            }
        }
    }
    this.solutionTemplates = (SolutionTemplate[]) org.vcell.util.BeanUtils.getArray(solutionTemplateList, SolutionTemplate.class);
}