Examples with Simulation cbit.vcell.solver.Simulation used on opensource projects

Example 36 with Simulation

use of cbit.vcell.solver.Simulation in project vcell by virtualcell.

the class MathTestingUtilities method getConstructedResultSet.

/**
 * Insert the method's description here.
 * Creation date: (1/17/2003 3:47:43 PM)
 * @return cbit.vcell.solver.ode.ODESolverResultSet
 * @param sim cbit.vcell.solver.Simulation
 */
public static ODESolverResultSet getConstructedResultSet(MathDescription mathDesc, double[] time) throws Exception {
    if (mathDesc.getGeometry().getDimension() != 0) {
        throw new RuntimeException("can only handle non-spatial simulations.");
    }
    Simulation sim = new Simulation(mathDesc);
    SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(sim, 0);
    ODESolverResultSet resultSet = new ODESolverResultSet();
    resultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
    for (int i = 0; i < time.length; i++) {
        resultSet.addRow(new double[] { time[i] });
    }
    java.util.Enumeration<SubDomain> subDomainEnum = mathDesc.getSubDomains();
    String errorString = "Variable(s) : ";
    while (subDomainEnum.hasMoreElements()) {
        SubDomain subDomain = subDomainEnum.nextElement();
        java.util.Enumeration<Equation> enumEquations = subDomain.getEquations();
        while (enumEquations.hasMoreElements()) {
            Equation equation = enumEquations.nextElement();
            Expression constructedSolution = equation.getExactSolution();
            if (constructedSolution != null) {
                constructedSolution = new Expression(constructedSolution);
                constructedSolution.bindExpression(simSymbolTable);
                constructedSolution = simSymbolTable.substituteFunctions(constructedSolution);
                constructedSolution = constructedSolution.flatten();
                resultSet.addFunctionColumn(new FunctionColumnDescription(constructedSolution, equation.getVariable().getName(), null, equation.getVariable().getName(), false));
            } else {
                errorString = errorString + equation.getVariable().getName() + ", ";
            }
        }
    }
    if (!errorString.equals("Variable(s) : ")) {
        throw new RuntimeException(errorString + " don't have a constructed solution");
    }
    return resultSet;
}

Example 37 with Simulation

use of cbit.vcell.solver.Simulation in project vcell by virtualcell.

the class MathTestingUtilities method getExactResultSet.

/**
 * Insert the method's description here.
 * Creation date: (1/17/2003 3:47:43 PM)
 * @return cbit.vcell.solver.ode.ODESolverResultSet
 * @param sim cbit.vcell.solver.Simulation
 */
public static ODESolverResultSet getExactResultSet(MathDescription mathDesc, double[] time, Constant sensitivityParam) throws Exception {
    if (mathDesc.getGeometry().getDimension() != 0) {
        throw new RuntimeException("can only handle non-spatial simulations.");
    }
    Simulation sim = new Simulation(mathDesc);
    SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(sim, 0);
    ODESolverResultSet resultSet = new ODESolverResultSet();
    resultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
    for (int i = 0; i < time.length; i++) {
        resultSet.addRow(new double[] { time[i] });
    }
    java.util.Enumeration<SubDomain> subDomainEnum = mathDesc.getSubDomains();
    while (subDomainEnum.hasMoreElements()) {
        SubDomain subDomain = subDomainEnum.nextElement();
        java.util.Enumeration<Equation> enumEquations = subDomain.getEquations();
        while (enumEquations.hasMoreElements()) {
            Equation equation = enumEquations.nextElement();
            Expression exactSolution = equation.getExactSolution();
            if (exactSolution != null) {
                exactSolution = new Expression(exactSolution);
                exactSolution.bindExpression(simSymbolTable);
                exactSolution = simSymbolTable.substituteFunctions(exactSolution);
                exactSolution.bindExpression(simSymbolTable);
                exactSolution = exactSolution.flatten();
                resultSet.addFunctionColumn(new FunctionColumnDescription(exactSolution, equation.getVariable().getName(), null, equation.getVariable().getName(), false));
                if (sensitivityParam != null) {
                    exactSolution = equation.getExactSolution();
                    Expression exactSensitivity = new Expression(exactSolution);
                    exactSensitivity.bindExpression(simSymbolTable);
                    exactSensitivity = simSymbolTable.substituteFunctions(exactSensitivity);
                    exactSensitivity.bindExpression(simSymbolTable);
                    exactSensitivity = exactSensitivity.differentiate(sensitivityParam.getName());
                    exactSensitivity = exactSensitivity.flatten();
                    VolVariable volVar = (VolVariable) equation.getVariable();
                    String sensName = SensVariable.getSensName(volVar, sensitivityParam);
                    resultSet.addFunctionColumn(new FunctionColumnDescription(exactSensitivity, sensName, null, sensName, false));
                }
            } else {
                throw new RuntimeException("variable " + equation.getVariable().getName() + " doesn't have an exact solution");
            }
        }
    }
    return resultSet;
}

Example 38 with Simulation

use of cbit.vcell.solver.Simulation in project vcell by virtualcell.

the class AbstractCompiledSolver method getProgress.

/**
 * Insert the method's description here.
 * Creation date: (6/28/01 2:48:52 PM)
 * @return double
 */
public double getProgress() {
    Simulation simulation = simTask.getSimulationJob().getSimulation();
    TimeBounds timeBounds = simulation.getSolverTaskDescription().getTimeBounds();
    double startTime = timeBounds.getStartingTime();
    double endTime = timeBounds.getEndingTime();
    return (currentTime - startTime) / (endTime - startTime);
}

Example 39 with Simulation

use of cbit.vcell.solver.Simulation in project vcell by virtualcell.

the class FVSolverStandalone method getChomboCommands.

private Collection<ExecutableCommand> getChomboCommands() {
    assert (isChombo);
    ArrayList<ExecutableCommand> commands = new ArrayList<ExecutableCommand>(2);
    String inputFilename = getInputFilename();
    String executableName = null;
    Simulation simulation = getSimulationJob().getSimulation();
    SolverTaskDescription sTaskDesc = simulation.getSolverTaskDescription();
    final boolean isParallel = sTaskDesc.isParallel();
    int dimension = simulation.getMeshSpecification().getGeometry().getDimension();
    switch(dimension) {
        case 2:
            try {
                executableName = SolverUtilities.getExes(SolverDescription.Chombo)[0].getAbsolutePath();
            } catch (IOException e) {
                throw new RuntimeException("failed to get executable for 2D solver " + SolverDescription.Chombo.getDisplayLabel() + ": " + e.getMessage(), e);
            }
            break;
        case 3:
            try {
                executableName = SolverUtilities.getExes(SolverDescription.Chombo)[1].getAbsolutePath();
            } catch (IOException e) {
                throw new RuntimeException("failed to get executable for 3D solver " + SolverDescription.Chombo.getDisplayLabel() + ": " + e.getMessage(), e);
            }
            break;
        default:
            throw new IllegalArgumentException("VCell Chombo solver does not support " + dimension + "problems");
    }
    if (isParallel) {
        String parallelName = executableName + "parallel";
        ExecutableCommand solve = new ExecutableCommand(new ExecutableCommand.LibraryPath(ResourceUtil.getLocalSolversDirectory().getAbsolutePath()), true, true, parallelName, inputFilename);
        commands.add(solve);
        ChomboSolverSpec css = sTaskDesc.getChomboSolverSpec();
        Objects.requireNonNull(css);
        if (css.isSaveVCellOutput()) {
            ExecutableCommand convertChomboData = new ExecutableCommand(new ExecutableCommand.LibraryPath(ResourceUtil.getLocalSolversDirectory().getAbsolutePath()), true, false, executableName, "-ccd", inputFilename);
            commands.add(convertChomboData);
        }
    } else {
        ExecutableCommand ec = new ExecutableCommand(new ExecutableCommand.LibraryPath(ResourceUtil.getLocalSolversDirectory().getAbsolutePath()), true, false, executableName, inputFilename);
        commands.add(ec);
        primaryCommand = ec;
    }
    return commands;
}

Example 40 with Simulation

use of cbit.vcell.solver.Simulation in project vcell by virtualcell.

the class FiniteVolumeFileWriter method write.

/**
 * Insert the method's description here.
 * Creation date: (5/9/2005 2:52:48 PM)
 * @throws MathException
 * @throws ExpressionException
 * @throws DataAccessException
 * @throws IOException
 */
public void write(String[] parameterNames) throws Exception {
    Variable[] originalVars = null;
    Simulation simulation = simTask.getSimulation();
    MathDescription mathDesc = simulation.getMathDescription();
    if (bChomboSolver) {
        writeJMSParamters();
        writeSimulationParamters();
        writeModelDescription();
        writeChomboSpec();
        writeVariables();
        writePostProcessingBlock();
        writeCompartments();
        writeMembranes();
    } else {
        if (simTask.getSimulation().isSerialParameterScan()) {
            originalVars = (Variable[]) BeanUtils.getArray(mathDesc.getVariables(), Variable.class);
            Variable[] allVars = (Variable[]) BeanUtils.getArray(mathDesc.getVariables(), Variable.class);
            MathOverrides mathOverrides = simulation.getMathOverrides();
            String[] scanParameters = mathOverrides.getOverridenConstantNames();
            for (int i = 0; i < scanParameters.length; i++) {
                String scanParameter = scanParameters[i];
                Variable mathVariable = mathDesc.getVariable(scanParameter);
                // 
                if (mathVariable instanceof Constant) {
                    Constant origConstant = (Constant) mathVariable;
                    for (int j = 0; j < allVars.length; j++) {
                        if (allVars[j].equals(origConstant)) {
                            allVars[j] = new ParameterVariable(origConstant.getName());
                            break;
                        }
                    }
                }
            }
            mathDesc.setAllVariables(allVars);
        }
        writeJMSParamters();
        writeSimulationParamters();
        writeModelDescription();
        writeMeshFile();
        writeVariables();
        if (mathDesc.isSpatialHybrid()) {
            writeSmoldyn();
        }
        writeParameters(parameterNames);
        writeSerialParameterScans();
        writeFieldData();
        writePostProcessingBlock();
        writeCompartments();
        writeMembranes();
        if (originalVars != null) {
            mathDesc.setAllVariables(originalVars);
        }
    }
}