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

Example 21 with MathDescription

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

Example 22 with MathDescription

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

the class FiniteVolumeFileWriter method writeSimulationParamters.

/**
 * @param timeFunction
 * @param startTime
 * @param endTime
 * @param rootFinder
 * @param uniqueRootTimes
 * @param bPrintIterations
 * @throws ExpressionException
 *
 * for testing within scrapbook, see below:
 *
 * try {
 *	edu.northwestern.at.utils.math.rootfinders.MonadicFunctionRootFinder rootFinder =
 *//			new edu.northwestern.at.utils.math.rootfinders.Brent();
 *			new edu.northwestern.at.utils.math.rootfinders.Bisection();
 *//			new edu.northwestern.at.utils.math.rootfinders.NewtonRaphson();
 *//			new edu.northwestern.at.utils.math.rootfinders.Secant();
 *	cbit.vcell.parser.SimpleSymbolTable simpleSymbolTable = new cbit.vcell.parser.SimpleSymbolTable(new String[] { "t" });
 *
 *	cbit.vcell.parser.Expression exp = new cbit.vcell.parser.Expression("t-0.56");
 *
 *	exp.bindExpression(simpleSymbolTable);
 *	java.util.TreeSet<Double> rootTimes = new java.util.TreeSet<Double>();
 *	double startTime = 0.0;
 *	double endTime = 100.0;
 *	System.out.print("exp = '"+ exp.infix() + "'");
 *	long currentTimeMS = System.currentTimeMillis();
 *	cbit.vcell.solvers.FiniteVolumeFileWriter.findAllRoots(exp,startTime,endTime,rootFinder,rootTimes,false);
 *	long finalTimeMS = System.currentTimeMillis();
 *	for (double root : rootTimes){
 *		System.out.println("root = "+root);
 *	}
 *	System.out.println("elapsedTime of computation = "+(finalTimeMS-currentTimeMS)+" ms, found " + rootTimes.size() + " roots (not unique)");
 *
 *}catch (Exception e){
 *	e.printStackTrace(System.out);
 *}
 */
/*public static void findAllRoots(Expression timeFunction, double startTime, double endTime, MonadicFunctionRootFinder rootFinder, TreeSet<Double> uniqueRootTimes, boolean bPrintIterations) throws ExpressionException{
	TreeSet<Double> allRootTimes = new TreeSet<Double>();
	final Expression function_exp = new Expression(timeFunction);
	MonadicFunction valueFunction = new MonadicFunction() {
		double[] values = new double[1];
		public double f(double t) {
			values[0] = t;
			try {
				return function_exp.evaluateVector(values);
			} catch (ExpressionException e) {
				e.printStackTrace();
				throw new RuntimeException("expression exception "+e.getMessage());
			}
		}
	};
	
	final Expression derivative_exp = new Expression(timeFunction.differentiate(ReservedVariable.TIME.getName()));
	MonadicFunction derivativeFunction = new MonadicFunction() {
		double[] values = new double[1];
		public double f(double t) {
			values[0] = t;
			try {
				return derivative_exp.evaluateVector(values);
			} catch (ExpressionException e) {
				e.printStackTrace();
				throw new RuntimeException("expression exception "+e.getMessage());
			}
		}
	};
	
	RootFinderConvergenceTest convergenceTest = new StandardRootFinderConvergenceTest();
	RootFinderIterationInformation iterationInformation = null;
	if (bPrintIterations){
		iterationInformation = new RootFinderIterationInformation() {				
			public void iterationInformation(double x, double fx, double dfx, int currentIteration) {
				System.out.println(currentIteration+") x="+x+", fx="+fx+", dfx="+dfx);
			}
		};
	}
	int NUM_BRACKETS = 1000;
	double simulationTime = endTime - startTime;
	double tolerance = simulationTime/1e10;
	int maxIter = 1000;
	
	for (int i=0;i<NUM_BRACKETS-1;i++){
		double bracketMin = startTime + simulationTime*i/NUM_BRACKETS;
		double bracketMax = startTime + simulationTime*(i+1)/NUM_BRACKETS;
	
		double root = rootFinder.findRoot(bracketMin, bracketMax, tolerance, maxIter, valueFunction, derivativeFunction, convergenceTest, iterationInformation);
		if (root>startTime && root<endTime && valueFunction.f(root)<=tolerance){
			allRootTimes.add(root);
		}
	}
	double uniqueTolerance = tolerance * 100;
	double lastUniqueRoot = Double.NEGATIVE_INFINITY;
	for (double root : allRootTimes){
		if (root-lastUniqueRoot > uniqueTolerance){
			uniqueRootTimes.add(root);
		}
		lastUniqueRoot = root;
	}

}  ---------------------------------JIM's CODE COMMENTTED FOR FUTURE DEVELOPMENT*/
/**
 *# Simulation Parameters
 *SIMULATION_PARAM_BEGIN
 *SOLVER SUNDIALS_PDE_SOLVER 1.0E-7 1.0E-9
 *DISCONTINUITY_TIMES 2 1.0E-4 3.0000000000000003E-4
 *BASE_FILE_NAME c:/Vcell/users/fgao/SimID_31746636_0_
 *ENDING_TIME 4.0E-4
 *KEEP_EVERY ONE_STEP 3
 *KEEP_AT_MOST 1000
 *SIMULATION_PARAM_END
 * @throws MathException
 * @throws ExpressionException
 */
private void writeSimulationParamters() throws ExpressionException, MathException {
    Simulation simulation = simTask.getSimulation();
    SolverTaskDescription solverTaskDesc = simulation.getSolverTaskDescription();
    printWriter.println("# Simulation Parameters");
    printWriter.println(FVInputFileKeyword.SIMULATION_PARAM_BEGIN);
    if (solverTaskDesc.getSolverDescription().equals(SolverDescription.SundialsPDE)) {
        printWriter.print(FVInputFileKeyword.SOLVER + " " + FVInputFileKeyword.SUNDIALS_PDE_SOLVER + " " + solverTaskDesc.getErrorTolerance().getRelativeErrorTolerance() + " " + solverTaskDesc.getErrorTolerance().getAbsoluteErrorTolerance() + " " + solverTaskDesc.getTimeStep().getMaximumTimeStep());
        if (simulation.getMathDescription().hasVelocity()) {
            printWriter.print(" " + solverTaskDesc.getSundialsPdeSolverOptions().getMaxOrderAdvection());
        }
        printWriter.println();
        Vector<Discontinuity> discontinuities = new Vector<Discontinuity>();
        TreeSet<Double> discontinuityTimes = new TreeSet<Double>();
        MathDescription mathDesc = simulation.getMathDescription();
        Enumeration<SubDomain> enum1 = mathDesc.getSubDomains();
        while (enum1.hasMoreElements()) {
            SubDomain sd = enum1.nextElement();
            Enumeration<Equation> enum_equ = sd.getEquations();
            while (enum_equ.hasMoreElements()) {
                Equation equation = enum_equ.nextElement();
                equation.getDiscontinuities(simTask.getSimulationJob().getSimulationSymbolTable(), discontinuities);
            }
        }
        getDiscontinuityTimes(discontinuities, discontinuityTimes);
        if (discontinuityTimes.size() > 0) {
            printWriter.print(FVInputFileKeyword.DISCONTINUITY_TIMES + " " + discontinuityTimes.size());
            for (double d : discontinuityTimes) {
                printWriter.print(" " + d);
            }
            printWriter.println();
        }
    } else if (solverTaskDesc.getSolverDescription().equals(SolverDescription.Chombo)) {
        printWriter.println(FVInputFileKeyword.SOLVER + " " + FVInputFileKeyword.CHOMBO_SEMIIMPLICIT_SOLVER);
    } else if (solverTaskDesc.getSolverDescription().equals(SolverDescription.VCellPetsc)) {
        printWriter.println(FVInputFileKeyword.SOLVER + " " + FVInputFileKeyword.VCELL_PETSC_SOLVER);
    } else {
        printWriter.println(FVInputFileKeyword.SOLVER + " " + FVInputFileKeyword.FV_SOLVER + " " + solverTaskDesc.getErrorTolerance().getRelativeErrorTolerance());
    }
    printWriter.println(FVInputFileKeyword.BASE_FILE_NAME + " " + new File(workingDirectory, simTask.getSimulationJob().getSimulationJobID()).getAbsolutePath());
    if (solverTaskDesc.isParallel() && destinationDirectory != null && !destinationDirectory.equals(workingDirectory)) {
        printWriter.println(FVInputFileKeyword.PRIMARY_DATA_DIR + " " + destinationDirectory.getAbsolutePath());
    }
    printWriter.println(FVInputFileKeyword.ENDING_TIME + " " + solverTaskDesc.getTimeBounds().getEndingTime());
    OutputTimeSpec outputTimeSpec = solverTaskDesc.getOutputTimeSpec();
    if (solverTaskDesc.getSolverDescription().isChomboSolver()) {
        List<TimeInterval> timeIntervalList = solverTaskDesc.getChomboSolverSpec().getTimeIntervalList();
        printWriter.println(FVInputFileKeyword.TIME_INTERVALS + " " + timeIntervalList.size());
        for (TimeInterval ti : timeIntervalList) {
            printWriter.println(ti.getEndingTime() + " " + ti.getTimeStep() + " " + ti.getKeepEvery());
        }
    } else if (solverTaskDesc.getSolverDescription().equals(SolverDescription.SundialsPDE)) {
        if (outputTimeSpec.isDefault()) {
            DefaultOutputTimeSpec defaultOutputTimeSpec = (DefaultOutputTimeSpec) outputTimeSpec;
            printWriter.println(FVInputFileKeyword.KEEP_EVERY + " " + FVInputFileKeyword.ONE_STEP + " " + defaultOutputTimeSpec.getKeepEvery());
            printWriter.println(FVInputFileKeyword.KEEP_AT_MOST + " " + defaultOutputTimeSpec.getKeepAtMost());
        } else {
            printWriter.println(FVInputFileKeyword.TIME_STEP + " " + ((UniformOutputTimeSpec) outputTimeSpec).getOutputTimeStep());
            printWriter.println(FVInputFileKeyword.KEEP_EVERY + " 1");
        }
    } else {
        double defaultTimeStep = solverTaskDesc.getTimeStep().getDefaultTimeStep();
        printWriter.println(FVInputFileKeyword.TIME_STEP + " " + defaultTimeStep);
        int keepEvery = 1;
        if (outputTimeSpec.isDefault()) {
            keepEvery = ((DefaultOutputTimeSpec) outputTimeSpec).getKeepEvery();
        } else if (outputTimeSpec.isUniform()) {
            UniformOutputTimeSpec uots = (UniformOutputTimeSpec) outputTimeSpec;
            double ots = uots.getOutputTimeStep();
            keepEvery = (int) Math.round(ots / defaultTimeStep);
        } else {
            throw new RuntimeException("unexpected OutputTime specification type :" + outputTimeSpec.getClass().getName());
        }
        if (keepEvery <= 0) {
            throw new RuntimeException("Output KeepEvery must be a positive integer. Try to change the output option.");
        }
        printWriter.println(FVInputFileKeyword.KEEP_EVERY + " " + keepEvery);
    }
    ErrorTolerance stopAtSpatiallyUniformErrorTolerance = solverTaskDesc.getStopAtSpatiallyUniformErrorTolerance();
    if (stopAtSpatiallyUniformErrorTolerance != null) {
        printWriter.println(FVInputFileKeyword.CHECK_SPATIALLY_UNIFORM + " " + stopAtSpatiallyUniformErrorTolerance.getAbsoluteErrorTolerance() + " " + stopAtSpatiallyUniformErrorTolerance.getRelativeErrorTolerance());
    }
    printWriter.println(FVInputFileKeyword.SIMULATION_PARAM_END);
    printWriter.println();
}

Example 23 with MathDescription

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

the class FiniteVolumeFileWriter method writeCompartments.

/**
 *COMPARTMENT_BEGIN nucleus
 *
 *BOUNDARY_CONDITIONS value value value value
 *
 *EQUATION_BEGIN rfB
 *INITIAL _VCell_FieldData_0;
 *RATE ( - (50.0 * rfB * ((x > -5.0) && (x < 5.0) && (y > -5.0) && (y < 5.0))) + (0.02 * ( - rB - rfB + (20.0 * ((x > -3.0) && (x < 3.0) && (y > -5.0) && (y < 5.0))) + _VCell_FieldData_0) * rf) - (0.1 * rfB));
 *EQUATION_END
 *
 *EQUATION_BEGIN r
 *INITIAL 5.0;
 *RATE ( - ((0.02 * r * ( - rB - rfB + (20.0 * ((x > -3.0) && (x < 3.0) && (y > -5.0) && (y < 5.0))) + _VCell_FieldData_0)) - (0.1 * rB)) + (50.0 * rf * ((x > -5.0) && (x < 5.0) && (y > -5.0) && (y < 5.0))));
 *DIFFUSION 10.0;
 *BOUNDARY_XM 5.0;
 *BOUNDARY_XP 5.0;
 *BOUNDARY_YM 5.0;
 *BOUNDARY_YP 5.0;
 *EQUATION_END
 *
 *COMPARTMENT_END
 * @throws ExpressionException
 * @throws MathException
 */
private void writeCompartments() throws ExpressionException, MathException {
    Simulation simulation = simTask.getSimulation();
    MathDescription mathDesc = simulation.getMathDescription();
    Enumeration<SubDomain> enum1 = mathDesc.getSubDomains();
    while (enum1.hasMoreElements()) {
        SubDomain sd = enum1.nextElement();
        if (sd instanceof CompartmentSubDomain) {
            CompartmentSubDomain csd = (CompartmentSubDomain) sd;
            printWriter.println("COMPARTMENT_BEGIN " + csd.getName());
            printWriter.println();
            writeCompartment_VarContext(csd);
            writeFastSystem(csd);
            printWriter.println("COMPARTMENT_END");
            printWriter.println();
        }
    }
    printWriter.println();
}

Example 24 with MathDescription

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

the class FiniteVolumeFileWriter method writeMembranes.

/**
 *MEMBRANE_BEGIN subVolume0_subVolume1_membrane subVolume0 subVolume1
 *
 *BOUNDARY_CONDITIONS value value value value
 *
 *EQUATION_BEGIN varMem
 *INITIAL (x > 0.75);
 *REACTION 0.0;
 *DIFFUSION 1.0;
 *BOUNDARY_XM (x > 0.75);
 *BOUNDARY_XP (x > 0.75);
 *BOUNDARY_YM (x > 0.75);
 *BOUNDARY_YP (x > 0.75);
 *EQUATION_END
 *
 *JUMP_CONDITION_BEGIN varVol
 *INFLUX 0.0;
 *OUTFLUX 0.0;
 *JUMP_CONDITION_END
 *
 *MEMBRANE_END
 * @throws ExpressionException
 * @throws MathException
 */
private void writeMembranes() throws ExpressionException, MathException {
    Simulation simulation = simTask.getSimulation();
    MathDescription mathDesc = simulation.getMathDescription();
    Enumeration<SubDomain> enum1 = mathDesc.getSubDomains();
    while (enum1.hasMoreElements()) {
        SubDomain sd = enum1.nextElement();
        if (sd instanceof MembraneSubDomain) {
            MembraneSubDomain msd = (MembraneSubDomain) sd;
            printWriter.println("MEMBRANE_BEGIN " + msd.getName() + " " + msd.getInsideCompartment().getName() + " " + msd.getOutsideCompartment().getName());
            printWriter.println();
            writeMembrane_VarContext(msd);
            writeMembrane_jumpConditions(msd);
            writeFastSystem(msd);
            printWriter.println("MEMBRANE_END");
            printWriter.println();
        }
    }
}

Example 25 with MathDescription

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

the class Simulation method setMathDescription.

/**
 * Insert the method's description here.
 * Creation date: (10/24/00 1:17:37 PM)
 * @param mathDesc cbit.vcell.math.MathDescription
 */
public void setMathDescription(MathDescription mathDescription) throws java.beans.PropertyVetoException {
    MathDescription oldValue = fieldMathDescription;
    fireVetoableChange("mathDescription", oldValue, mathDescription);
    fieldMathDescription = mathDescription;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(this);
    }
    if (fieldMathDescription != null) {
        fieldMathDescription.removePropertyChangeListener(this);
        fieldMathDescription.addPropertyChangeListener(this);
    }
    refreshMeshSpec();
    // 
    if (mathDescription != null && getMathOverrides() != null) {
        getMathOverrides().updateFromMathDescription();
    }
    // 
    if (oldValue == null || mathDescription == null || oldValue.isSpatial() != mathDescription.isSpatial()) {
        fieldSolverTaskDescription = new SolverTaskDescription(this);
    }
    firePropertyChange("mathDescription", oldValue, mathDescription);
}