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

Example 6 with SolverTaskDescription

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

the class OutputOptionsPanel method setSolverTaskDescription.

/**
 * set solver description. The contained {@link SolverTaskDescription#getSimulation()}
 * is usually a temporary cloned object with  a null {@link SimulationOwner}  ; therefore
 * we required the {@link UnitInfo} of the actual {@link Simulation} owner as a parameter
 * @param newValue
 * @param unitInfo not null
 */
public final void setSolverTaskDescription(SolverTaskDescription newValue, UnitInfo unitInfo) {
    Objects.requireNonNull(unitInfo);
    SolverTaskDescription oldValue = solverTaskDescription;
    /* Stop listening for events from the current object */
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(ivjEventHandler);
    }
    solverTaskDescription = newValue;
    /* Listen for events from the new object */
    if (newValue != null) {
        newValue.addPropertyChangeListener(ivjEventHandler);
    }
    solverTaskDescription = newValue;
    chomboOutputOptionsPanel.setSolverTaskDescription(solverTaskDescription);
    firePropertyChange("solverTaskDescription", oldValue, newValue);
    getOutputTimeStepTextField().addFocusListener(ivjEventHandler);
    getDefaultOutputRadioButton().addActionListener(ivjEventHandler);
    getUniformOutputRadioButton().addActionListener(ivjEventHandler);
    getExplicitOutputRadioButton().addActionListener(ivjEventHandler);
    getKeepEveryTextField().addFocusListener(ivjEventHandler);
    getKeepAtMostTextField().addFocusListener(ivjEventHandler);
    getOutputTimesTextField().addFocusListener(ivjEventHandler);
    getOutputTimeStepTextField().setInputVerifier(new InputVerifier() {

        @Override
        public boolean verify(JComponent input) {
            return false;
        }

        @Override
        public boolean shouldYieldFocus(JComponent input) {
            boolean bValid = true;
            try {
                double outputTime = Double.parseDouble(getOutputTimeStepTextField().getText());
                if (solverTaskDescription.getOutputTimeSpec().isUniform() && !solverTaskDescription.getSolverDescription().hasVariableTimestep()) {
                    double timeStep = solverTaskDescription.getTimeStep().getDefaultTimeStep();
                    double suggestedInterval = outputTime;
                    if (outputTime < timeStep) {
                        suggestedInterval = timeStep;
                        bValid = false;
                    } else if (!BeanUtils.isIntegerMultiple(outputTime, timeStep)) {
                        double n = outputTime / timeStep;
                        int intn = (int) Math.round(n);
                        if (intn != n) {
                            bValid = false;
                            suggestedInterval = (intn * timeStep);
                        }
                    }
                    if (!bValid) {
                        String ret = PopupGenerator.showWarningDialog(OutputOptionsPanel.this, "Output Interval", "Output Interval must " + "be integer multiple of time step.\n\nChange Output Interval to " + suggestedInterval + "?", new String[] { UserMessage.OPTION_YES, UserMessage.OPTION_NO }, UserMessage.OPTION_YES);
                        if (ret.equals(UserMessage.OPTION_YES)) {
                            getOutputTimeStepTextField().setText(suggestedInterval + "");
                            bValid = true;
                        }
                    }
                }
            } catch (NumberFormatException ex) {
                DialogUtils.showErrorDialog(OutputOptionsPanel.this, "Wrong number format " + ex.getMessage().toLowerCase());
                bValid = false;
            }
            if (bValid) {
                getOutputTimeStepTextField().setBorder(UIManager.getBorder("TextField.border"));
            } else {
                getOutputTimeStepTextField().setBorder(GuiConstants.ProblematicTextFieldBorder);
                SwingUtilities.invokeLater(new Runnable() {

                    public void run() {
                        getOutputTimeStepTextField().requestFocus();
                    }
                });
            }
            return bValid;
        }
    });
    getOutputTimesTextField().setInputVerifier(new InputVerifier() {

        @Override
        public boolean verify(JComponent input) {
            return false;
        }

        @Override
        public boolean shouldYieldFocus(JComponent input) {
            ExplicitOutputTimeSpec eots = ExplicitOutputTimeSpec.fromString(getOutputTimesTextField().getText());
            return checkExplicitOutputTimes(eots);
        }
    });
    // set time label units
    JLabel timeUnitsLabel = getTimeStepUnitsLabel();
    timeUnitsLabel.setText(unitInfo.getTimeUnitString());
}

Example 7 with SolverTaskDescription

use of cbit.vcell.solver.SolverTaskDescription 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 8 with SolverTaskDescription

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

the class SundialsPdeSolverOptionsPanel method setSolverTaskDescription.

public final void setSolverTaskDescription(SolverTaskDescription newValue) {
    SolverTaskDescription oldValue = solverTaskDescription;
    /* Stop listening for events from the current object */
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(ivjEventHandler);
    }
    solverTaskDescription = newValue;
    /* Listen for events from the new object */
    if (newValue != null) {
        newValue.addPropertyChangeListener(ivjEventHandler);
    }
    solverTaskDescription = newValue;
    refresh();
}

Example 9 with SolverTaskDescription

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

the class TimeStepPanel method setSolverTaskDescription.

/**
 * Sets the timeStep property (cbit.vcell.solver.TimeStep) value.
 * @param timeStep The new value for the property.
 * @exception java.beans.PropertyVetoException The exception description.
 * @see #getTimeStep
 */
public void setSolverTaskDescription(SolverTaskDescription newValue) throws java.beans.PropertyVetoException {
    SolverTaskDescription oldValue = solverTaskDescription;
    /* Stop listening for events from the current object */
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(ivjEventHandler);
    }
    solverTaskDescription = newValue;
    /* Listen for events from the new object */
    if (newValue != null) {
        newValue.addPropertyChangeListener(ivjEventHandler);
    }
    solverTaskDescription = newValue;
    firePropertyChange("solverTaskDescription", oldValue, newValue);
    initConnections();
}

Example 10 with SolverTaskDescription

use of cbit.vcell.solver.SolverTaskDescription 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;
}