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

Example 6 with TimeBounds

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

the class ClientTaskManager method changeEndTime.

public static void changeEndTime(JComponent requester, SolverTaskDescription solverTaskDescription, double newEndTime) throws PropertyVetoException {
    TimeBounds oldTimeBounds = solverTaskDescription.getTimeBounds();
    TimeBounds timeBounds = new TimeBounds(oldTimeBounds.getStartingTime(), newEndTime);
    solverTaskDescription.setTimeBounds(timeBounds);
    if (solverTaskDescription.getOutputTimeSpec() instanceof UniformOutputTimeSpec) {
        UniformOutputTimeSpec uniformOutputTimeSpec = (UniformOutputTimeSpec) solverTaskDescription.getOutputTimeSpec();
        if (timeBounds.getEndingTime() < uniformOutputTimeSpec.getOutputTimeStep()) {
            double outputTime = solverTaskDescription.getTimeBounds().getEndingTime() / 20.0;
            String ret = PopupGenerator.showWarningDialog(requester, "Output Interval", "Output interval(" + uniformOutputTimeSpec.getOutputTimeStep() + "s) is greater than end time(" + timeBounds.getEndingTime() + "s) which will not output any results. Do you want to change " + "output interval to every " + outputTime + "s (20 time points)?\n\nIf not, output interval will change to " + timeBounds.getEndingTime() + "s(the end time).", new String[] { UserMessage.OPTION_YES, UserMessage.OPTION_NO }, UserMessage.OPTION_YES);
            if (ret.equals(UserMessage.OPTION_YES)) {
                solverTaskDescription.setOutputTimeSpec(new UniformOutputTimeSpec(outputTime));
            } else {
                solverTaskDescription.setOutputTimeSpec(new UniformOutputTimeSpec(timeBounds.getEndingTime()));
            }
        }
    }
}

Example 7 with TimeBounds

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

the class OutputOptionsPanel method checkExplicitOutputTimes.

private boolean checkExplicitOutputTimes(ExplicitOutputTimeSpec ots) {
    boolean bValid = true;
    double startingTime = solverTaskDescription.getTimeBounds().getStartingTime();
    double endingTime = solverTaskDescription.getTimeBounds().getEndingTime();
    double[] times = ((ExplicitOutputTimeSpec) ots).getOutputTimes();
    if (times[0] < startingTime || times[times.length - 1] > endingTime) {
        bValid = false;
        String ret = PopupGenerator.showWarningDialog(OutputOptionsPanel.this, "Output times should be within [" + startingTime + "," + endingTime + "].\n\nChange ENDING TIME to " + times[times.length - 1] + "?", new String[] { UserMessage.OPTION_YES, UserMessage.OPTION_NO }, UserMessage.OPTION_YES);
        if (ret.equals(UserMessage.OPTION_YES)) {
            try {
                solverTaskDescription.setTimeBounds(new TimeBounds(startingTime, times[times.length - 1]));
                bValid = true;
            } catch (PropertyVetoException e) {
                e.printStackTrace(System.out);
                DialogUtils.showErrorDialog(OutputOptionsPanel.this, e.getMessage());
            }
        }
    }
    if (bValid) {
        getOutputTimesTextField().setBorder(UIManager.getBorder("TextField.border"));
    } else {
        getOutputTimesTextField().setBorder(GuiConstants.ProblematicTextFieldBorder);
        javax.swing.SwingUtilities.invokeLater(new Runnable() {

            public void run() {
                getOutputTimesTextField().requestFocus();
            }
        });
    }
    return bValid;
}

Example 8 with TimeBounds

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

the class SimulationSummaryPanel method displayTask.

/**
 * Comment
 */
private void displayTask() {
    SolverTaskDescription solverTaskDescription = getSimulation().getSolverTaskDescription();
    try {
        NonspatialStochSimOptions stochOpt = solverTaskDescription.getStochOpt();
        if (stochOpt != null && stochOpt.getNumOfTrials() > 1) {
            getJLabelOutput().setText("Histogram with " + stochOpt.getNumOfTrials() + " Trials(@last time point)");
        } else {
            // gcwtodo
            String text = solverTaskDescription.getOutputTimeSpec().getShortDescription();
            if (solverTaskDescription.getSolverDescription().isChomboSolver()) {
                text = "Variable";
                if (solverTaskDescription.getChomboSolverSpec().getTimeIntervalList().size() == 1) {
                    text = "Every " + solverTaskDescription.getChomboSolverSpec().getLastTimeInterval().getOutputTimeStep() + "s";
                }
            } else if (solverTaskDescription.getOutputTimeSpec().isDefault() && !solverTaskDescription.getSolverDescription().isSemiImplicitPdeSolver() && !solverTaskDescription.getSolverDescription().equals(SolverDescription.StochGibson)) {
                text += ", at most " + ((DefaultOutputTimeSpec) solverTaskDescription.getOutputTimeSpec()).getKeepAtMost();
            }
            getJLabelOutput().setText(text);
        }
    } catch (Exception exc) {
        exc.printStackTrace(System.out);
        getJLabelOutput().setText("");
    }
    SolverDescription solverDescription = solverTaskDescription.getSolverDescription();
    try {
        ErrorTolerance errorTolerance = solverTaskDescription.getErrorTolerance();
        TimeStep timeStep = solverTaskDescription.getTimeStep();
        getJLabelRelTol().setText("Rel tol");
        getJLabelAbsTol().setText("Abs tol");
        getJLabel12().setText("Timestep");
        getJLabelRelTol().setEnabled(false);
        getJLabelAbsTol().setEnabled(false);
        getJLabel12().setEnabled(false);
        getJLabel10().setText("Sensitivity Analysis");
        getJLabel10().setEnabled(true);
        if (solverDescription.equals(SolverDescription.StochGibson)) {
            getJLabel12().setEnabled(false);
            getJLabelTimestep().setText("");
        } else if (solverDescription.equals(SolverDescription.NFSim)) {
            TimeBounds tb = solverTaskDescription.getTimeBounds();
            double dtime = tb.getEndingTime() - tb.getStartingTime();
            if (solverTaskDescription.getOutputTimeSpec() instanceof UniformOutputTimeSpec) {
                UniformOutputTimeSpec uots = (UniformOutputTimeSpec) solverTaskDescription.getOutputTimeSpec();
                double interval = uots.getOutputTimeStep();
                int steps = (int) Math.round(dtime / interval);
                getJLabel12().setEnabled(true);
                getJLabel12().setText("Timepoints");
                getJLabelTimestep().setText(steps + "");
            } else if (solverTaskDescription.getOutputTimeSpec() instanceof DefaultOutputTimeSpec) {
                DefaultOutputTimeSpec uots = (DefaultOutputTimeSpec) solverTaskDescription.getOutputTimeSpec();
                getJLabel12().setEnabled(true);
                getJLabel12().setText("End Time");
                getJLabelTimestep().setText(solverTaskDescription.getTimeBounds().getEndingTime() + "");
            } else {
                getJLabel12().setEnabled(false);
                getJLabel12().setText("End Time");
                getJLabelTimestep().setText("na");
            }
            NFsimSimulationOptions nfsso = solverTaskDescription.getNFSimSimulationOptions();
            String utl = "default";
            Integer moleculeDistance = nfsso.getMoleculeDistance();
            if (moleculeDistance != null) {
                utl = moleculeDistance + "";
            }
            getJLabelRelTol().setEnabled(true);
            getJLabelRelTol().setText("Universal Transversal Limit");
            getJLabelRelTolValue().setText(utl);
            String gml = "default";
            Integer maxMoleculesPerType = nfsso.getMaxMoleculesPerType();
            if (maxMoleculesPerType != null) {
                gml = maxMoleculesPerType + "";
            }
            getJLabelAbsTol().setEnabled(true);
            getJLabelAbsTol().setText("Max # of each " + MolecularType.typeName);
            getJLabelAbsTolValue().setText(gml);
        } else if (solverDescription.isNonSpatialStochasticSolver()) {
            getJLabel12().setEnabled(true);
            getJLabel12().setText("Timestep");
            getJLabelTimestep().setText(timeStep.getDefaultTimeStep() + "s");
        } else if (solverDescription.hasVariableTimestep()) {
            getJLabel12().setEnabled(true);
            getJLabel12().setText("Max timestep");
            getJLabelTimestep().setText(timeStep.getMaximumTimeStep() + "s");
            getJLabelRelTol().setEnabled(true);
            getJLabelRelTolValue().setText("" + errorTolerance.getRelativeErrorTolerance());
            getJLabelAbsTol().setEnabled(true);
            getJLabelAbsTolValue().setText("" + errorTolerance.getAbsoluteErrorTolerance());
        } else {
            getJLabel12().setEnabled(true);
            getJLabel12().setText("Timestep");
            if (solverDescription.isChomboSolver()) {
                String text = "Variable";
                if (solverTaskDescription.getChomboSolverSpec().getTimeIntervalList().size() == 1) {
                    text = solverTaskDescription.getChomboSolverSpec().getLastTimeInterval().getTimeStep() + "s";
                }
                getJLabelTimestep().setText(text);
            } else {
                getJLabelTimestep().setText(timeStep.getDefaultTimeStep() + "s");
            }
            if (solverDescription.isSemiImplicitPdeSolver()) {
                getJLabelRelTol().setEnabled(true);
                getJLabelRelTolValue().setText("" + errorTolerance.getRelativeErrorTolerance());
            } else {
                getJLabelRelTol().setEnabled(false);
                getJLabelRelTolValue().setText("");
            }
            getJLabelAbsTol().setEnabled(false);
            getJLabelAbsTolValue().setText("");
        }
    } catch (Exception exc) {
        exc.printStackTrace(System.out);
        getJLabelTimestep().setText("");
        getJLabelRelTolValue().setText("");
        getJLabelAbsTolValue().setText("");
    }
    try {
        boolean bChomboSolver = solverDescription.isChomboSolver();
        getJLabelTitleNumProcessors().setVisible(bChomboSolver);
        getJLabelNumProcessors().setVisible(bChomboSolver);
        if (bChomboSolver) {
            getJLabelNumProcessors().setText(String.valueOf(solverTaskDescription.getNumProcessors()));
        }
        if (getSimulation().isSpatial() || solverDescription.isNonSpatialStochasticSolver()) {
            getJLabelSensitivity().setVisible(false);
            getJLabel10().setVisible(false);
        } else if (solverDescription.equals(SolverDescription.NFSim)) {
            getJLabel10().setText("On-the-fly observ comp.");
            NFsimSimulationOptions nfsso = solverTaskDescription.getNFSimSimulationOptions();
            boolean goc = nfsso.getObservableComputationOff();
            getJLabelSensitivity().setText(goc + "");
        } else {
            getJLabelSensitivity().setVisible(true);
            getJLabel10().setVisible(true);
            Constant param = solverTaskDescription.getSensitivityParameter();
            if (param == null) {
                getJLabelSensitivity().setText("no");
            } else {
                getJLabelSensitivity().setText(param.getName());
            }
        }
    } catch (Exception exc) {
        exc.printStackTrace(System.out);
        getJLabelSensitivity().setText("");
    }
    if (solverDescription.isNonSpatialStochasticSolver()) {
        getJLabelRelTol().setVisible(false);
        getJLabelAbsTol().setVisible(false);
        getJLabelRelTolValue().setVisible(false);
        getJLabelAbsTolValue().setVisible(false);
    } else {
        getJLabelRelTol().setVisible(true);
        getJLabelAbsTol().setVisible(true);
    }
}

Example 9 with TimeBounds

use of cbit.vcell.solver.TimeBounds 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 10 with TimeBounds

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

the class DefaultODESolver method updateResultSet.

/**
 * This method was created by a SmartGuide.
 */
protected final void updateResultSet() throws IOException, ExpressionException {
    ODESolverResultSet results = getODESolverResultSet();
    synchronized (results) {
        // so that we don't mess up when saving or reading intermediate results; performance penalty minimal
        double[] valueVector = getValueVector(0);
        // one extra index for time.
        double[] values = new double[getStateVariableCount() + 1];
        for (int i = 0; i < getStateVariableCount(); i++) {
            int c = results.findColumn(getStateVariable(i).getVariable().getName());
            // cbit.util.Assertion.assert(c >= 0 && c < results.getDataColumnCount());
            values[c] = valueVector[getVariableIndex(i)];
        }
        values[ReservedVariable.TIME.getIndex()] = getCurrentTime();
        results.addRow(values);
    }
    // setSolverStatus(new SolverStatus (SolverStatus.SOLVER_RUNNING));
    Simulation sim = simTask.getSimulation();
    double t = getCurrentTime();
    TimeBounds timeBounds = sim.getSolverTaskDescription().getTimeBounds();
    double t0 = timeBounds.getStartingTime();
    double t1 = timeBounds.getEndingTime();
    printToFile((t - t0) / (t1 - t0));
}