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

Example 6 with ExplicitOutputTimeSpec

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

the class ITextWriter method writeSimulation.

// container can be a chapter or a section of a chapter.
protected void writeSimulation(Section container, Simulation sim) throws DocumentException {
    if (sim == null) {
        return;
    }
    Section simSection = container.addSection(sim.getName(), container.numberDepth() + 1);
    writeMetadata(simSection, sim.getName(), sim.getDescription(), null, "Simulation ");
    // add overriden params
    Table overParamTable = null;
    MathOverrides mo = sim.getMathOverrides();
    if (mo != null) {
        String[] constants = mo.getOverridenConstantNames();
        for (int i = 0; i < constants.length; i++) {
            String actualStr = "", defStr = "";
            Expression tempExp = mo.getDefaultExpression(constants[i]);
            if (tempExp != null) {
                defStr = tempExp.infix();
            }
            if (mo.isScan(constants[i])) {
                actualStr = mo.getConstantArraySpec(constants[i]).toString();
            } else {
                tempExp = mo.getActualExpression(constants[i], 0);
                if (tempExp != null) {
                    actualStr = tempExp.infix();
                }
            }
            if (overParamTable == null) {
                overParamTable = getTable(3, 75, 1, 3, 3);
                overParamTable.setAlignment(Table.ALIGN_LEFT);
                overParamTable.addCell(createCell("Overriden Parameters", getBold(DEF_HEADER_FONT_SIZE), 3, 1, Element.ALIGN_CENTER, true));
                overParamTable.addCell(createHeaderCell("Name", getBold(), 1));
                overParamTable.addCell(createHeaderCell("Actual Value", getBold(), 1));
                overParamTable.addCell(createHeaderCell("Default Value", getBold(), 1));
            }
            overParamTable.addCell(createCell(constants[i], getFont()));
            overParamTable.addCell(createCell(actualStr, getFont()));
            overParamTable.addCell(createCell(defStr, getFont()));
        }
    }
    if (overParamTable != null) {
        simSection.add(overParamTable);
    }
    // add spatial details
    // sim.isSpatial();
    Table meshTable = null;
    MeshSpecification mesh = sim.getMeshSpecification();
    if (mesh != null) {
        Geometry geom = mesh.getGeometry();
        Extent extent = geom.getExtent();
        String extentStr = "(" + extent.getX() + ", " + extent.getY() + ", " + extent.getZ() + ")";
        ISize meshSize = mesh.getSamplingSize();
        String meshSizeStr = "(" + meshSize.getX() + ", " + meshSize.getY() + ", " + meshSize.getZ() + ")";
        meshTable = getTable(2, 75, 1, 3, 3);
        meshTable.setAlignment(Table.ALIGN_LEFT);
        meshTable.addCell(createCell("Geometry Setting", getBold(DEF_HEADER_FONT_SIZE), 2, 1, Element.ALIGN_CENTER, true));
        meshTable.addCell(createCell("Geometry Size (um)", getFont()));
        meshTable.addCell(createCell(extentStr, getFont()));
        meshTable.addCell(createCell("Mesh Size (elements)", getFont()));
        meshTable.addCell(createCell(meshSizeStr, getFont()));
    }
    if (meshTable != null) {
        simSection.add(meshTable);
    }
    // write advanced sim settings
    Table simAdvTable = null;
    SolverTaskDescription solverDesc = sim.getSolverTaskDescription();
    if (solverDesc != null) {
        String solverName = solverDesc.getSolverDescription().getDisplayLabel();
        simAdvTable = getTable(2, 75, 1, 3, 3);
        simAdvTable.setAlignment(Table.ALIGN_LEFT);
        simAdvTable.addCell(createCell("Advanced Settings", getBold(DEF_HEADER_FONT_SIZE), 2, 1, Element.ALIGN_CENTER, true));
        simAdvTable.addCell(createCell("Solver Name", getFont()));
        simAdvTable.addCell(createCell(solverName, getFont()));
        simAdvTable.addCell(createCell("Time Bounds - Starting", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeBounds().getStartingTime(), getFont()));
        simAdvTable.addCell(createCell("Time Bounds - Ending", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeBounds().getEndingTime(), getFont()));
        simAdvTable.addCell(createCell("Time Step - Min", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeStep().getMinimumTimeStep(), getFont()));
        simAdvTable.addCell(createCell("Time Step - Default", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeStep().getDefaultTimeStep(), getFont()));
        simAdvTable.addCell(createCell("Time Step - Max", getFont()));
        simAdvTable.addCell(createCell("" + solverDesc.getTimeStep().getMaximumTimeStep(), getFont()));
        ErrorTolerance et = solverDesc.getErrorTolerance();
        if (et != null) {
            simAdvTable.addCell(createCell("Error Tolerance - Absolute", getFont()));
            simAdvTable.addCell(createCell("" + et.getAbsoluteErrorTolerance(), getFont()));
            simAdvTable.addCell(createCell("Error Tolerance - Relative", getFont()));
            simAdvTable.addCell(createCell("" + et.getRelativeErrorTolerance(), getFont()));
        }
        OutputTimeSpec ots = solverDesc.getOutputTimeSpec();
        if (ots.isDefault()) {
            simAdvTable.addCell(createCell("Keep Every", getFont()));
            simAdvTable.addCell(createCell("" + ((DefaultOutputTimeSpec) ots).getKeepEvery(), getFont()));
            simAdvTable.addCell(createCell("Keep At Most", getFont()));
            simAdvTable.addCell(createCell("" + ((DefaultOutputTimeSpec) ots).getKeepAtMost(), getFont()));
        } else if (ots.isUniform()) {
            simAdvTable.addCell(createCell("Output Time Step", getFont()));
            simAdvTable.addCell(createCell("" + ((UniformOutputTimeSpec) ots).getOutputTimeStep(), getFont()));
        } else if (ots.isExplicit()) {
            simAdvTable.addCell(createCell("Output Time Points", getFont()));
            simAdvTable.addCell(createCell("" + ((ExplicitOutputTimeSpec) ots).toCommaSeperatedOneLineOfString(), getFont()));
        }
        simAdvTable.addCell(createCell("Use Symbolic Jacobian (T/F)", getFont()));
        simAdvTable.addCell(createCell((solverDesc.getUseSymbolicJacobian() ? " T " : " F "), getFont()));
        Constant sp = solverDesc.getSensitivityParameter();
        if (sp != null) {
            simAdvTable.addCell(createCell("Sensitivity Analysis Param", getFont()));
            simAdvTable.addCell(createCell(sp.getName(), getFont()));
        }
    }
    if (simAdvTable != null) {
        simSection.add(simAdvTable);
    }
}

Example 7 with ExplicitOutputTimeSpec

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

the class OutputOptionsPanel method actionOutputOptionButtonState.

private void actionOutputOptionButtonState(java.awt.event.ActionEvent actionEvent) {
    try {
        if (solverTaskDescription == null) {
            return;
        }
        OutputTimeSpec outputTimeSpec = solverTaskDescription.getOutputTimeSpec();
        if (actionEvent.getSource() == getDefaultOutputRadioButton() && !outputTimeSpec.isDefault()) {
            solverTaskDescription.setOutputTimeSpec(new DefaultOutputTimeSpec());
        } else if (actionEvent.getSource() == getUniformOutputRadioButton() && !outputTimeSpec.isUniform()) {
            double outputTime = 0.0;
            if (solverTaskDescription.getSolverDescription().isSemiImplicitPdeSolver()) {
                String floatStr = "" + (float) (((DefaultOutputTimeSpec) outputTimeSpec).getKeepEvery() * solverTaskDescription.getTimeStep().getDefaultTimeStep());
                outputTime = Double.parseDouble(floatStr);
            } else {
                TimeBounds timeBounds = solverTaskDescription.getTimeBounds();
                Range outputTimeRange = NumberUtils.getDecimalRange(timeBounds.getStartingTime(), timeBounds.getEndingTime() / 100, true, true);
                outputTime = outputTimeRange.getMax();
            }
            solverTaskDescription.setOutputTimeSpec(new UniformOutputTimeSpec(outputTime));
        } else if (actionEvent.getSource() == getExplicitOutputRadioButton() && !outputTimeSpec.isExplicit()) {
            TimeBounds timeBounds = solverTaskDescription.getTimeBounds();
            solverTaskDescription.setOutputTimeSpec(new ExplicitOutputTimeSpec(new double[] { timeBounds.getStartingTime(), timeBounds.getEndingTime() }));
        }
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 8 with ExplicitOutputTimeSpec

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

the class SimulationListTableModel method setValueAt.

/**
 * Insert the method's description here.
 * Creation date: (7/12/2004 2:01:23 PM)
 * @param aValue java.lang.Object
 * @param rowIndex int
 * @param columnIndex int
 */
public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    Simulation simulation = getValueAt(rowIndex);
    try {
        switch(columnIndex) {
            case COLUMN_NAME:
                if (aValue instanceof String) {
                    String newName = (String) aValue;
                    if (!simulation.getName().equals(newName)) {
                        simulation.setName(newName);
                    }
                }
                break;
            case COLUMN_ENDTIME:
                if (aValue instanceof Double) {
                    SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
                    double newEndTime = (Double) aValue;
                    if (newEndTime != solverTaskDescription.getTimeBounds().getEndingTime()) {
                        ClientTaskManager.changeEndTime(ownerTable, solverTaskDescription, newEndTime);
                        simulation.setIsDirty(true);
                    }
                }
                break;
            case COLUMN_OUTPUT:
                if (aValue instanceof String) {
                    SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
                    OutputTimeSpec ots = solverTaskDescription.getOutputTimeSpec();
                    OutputTimeSpec newOts = null;
                    if (ots instanceof DefaultOutputTimeSpec) {
                        int newValue = Integer.parseInt((String) aValue);
                        newOts = new DefaultOutputTimeSpec(newValue, ((DefaultOutputTimeSpec) ots).getKeepAtMost());
                    } else if (ots instanceof UniformOutputTimeSpec) {
                        try {
                            boolean bValid = true;
                            double outputTime = Double.parseDouble((String) aValue);
                            if (solverTaskDescription.getOutputTimeSpec().isUniform()) {
                                if (solverTaskDescription.getSolverDescription().hasVariableTimestep()) {
                                    newOts = new UniformOutputTimeSpec(outputTime);
                                } else {
                                    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);
                                            suggestedInterval = (intn * timeStep);
                                            if (suggestedInterval != outputTime) {
                                                bValid = false;
                                            }
                                        }
                                    }
                                    if (bValid) {
                                        newOts = new UniformOutputTimeSpec(outputTime);
                                    } else {
                                        String ret = PopupGenerator.showWarningDialog(ownerTable, "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)) {
                                            newOts = new UniformOutputTimeSpec(suggestedInterval);
                                        }
                                    }
                                }
                            }
                        } catch (NumberFormatException ex) {
                            DialogUtils.showErrorDialog(ownerTable, "Wrong number format " + ex.getMessage().toLowerCase());
                        }
                    } else if (ots instanceof ExplicitOutputTimeSpec) {
                        newOts = ExplicitOutputTimeSpec.fromString((String) aValue);
                    }
                    if (newOts != null && !newOts.compareEqual(ots)) {
                        solverTaskDescription.setOutputTimeSpec(newOts);
                        simulation.setIsDirty(true);
                    }
                }
                break;
        }
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
        PopupGenerator.showErrorDialog(ownerTable, ex.getMessage());
    }
}

Example 9 with ExplicitOutputTimeSpec

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

the class OdeFileWriter method write.

/**
 * Insert the method's description here.
 * Creation date: (3/8/00 10:31:52 PM)
 */
public void write(String[] parameterNames) throws Exception {
    createStateVariables();
    createSymbolTable();
    Simulation simulation = simTask.getSimulation();
    if (simulation.getSolverTaskDescription().getUseSymbolicJacobian()) {
        throw new RuntimeException("symbolic jacobian option not yet supported in interpreted Stiff solver");
    }
    writeJMSParamters();
    SolverTaskDescription solverTaskDescription = simulation.getSolverTaskDescription();
    TimeBounds timeBounds = solverTaskDescription.getTimeBounds();
    ErrorTolerance errorTolerance = solverTaskDescription.getErrorTolerance();
    printWriter.println("SOLVER " + getSolverName());
    printWriter.println("STARTING_TIME " + timeBounds.getStartingTime());
    printWriter.println("ENDING_TIME " + timeBounds.getEndingTime());
    printWriter.println("RELATIVE_TOLERANCE " + errorTolerance.getRelativeErrorTolerance());
    printWriter.println("ABSOLUTE_TOLERANCE " + errorTolerance.getAbsoluteErrorTolerance());
    printWriter.println("MAX_TIME_STEP " + simulation.getSolverTaskDescription().getTimeStep().getMaximumTimeStep());
    OutputTimeSpec ots = simulation.getSolverTaskDescription().getOutputTimeSpec();
    if (ots.isDefault()) {
        printWriter.println("KEEP_EVERY " + ((DefaultOutputTimeSpec) ots).getKeepEvery());
    } else if (ots.isUniform()) {
        printWriter.println("OUTPUT_TIME_STEP " + ((UniformOutputTimeSpec) ots).getOutputTimeStep());
    } else if (ots.isExplicit()) {
        printWriter.println("OUTPUT_TIMES " + ((ExplicitOutputTimeSpec) ots).getNumTimePoints());
        printWriter.println(((ExplicitOutputTimeSpec) ots).toSpaceSeperatedMultiLinesOfString());
    }
    if (parameterNames != null && parameterNames.length != 0) {
        printWriter.println("NUM_PARAMETERS " + parameterNames.length);
        for (int i = 0; i < parameterNames.length; i++) {
            printWriter.println(parameterNames[i]);
        }
    }
    HashMap<Discontinuity, String> discontinuityNameMap = new HashMap<Discontinuity, String>();
    String eventString = null;
    if (simulation.getMathDescription().hasEvents()) {
        eventString = writeEvents(discontinuityNameMap);
    }
    String equationString = writeEquations(discontinuityNameMap);
    if (discontinuityNameMap.size() > 0) {
        printWriter.println("DISCONTINUITIES " + discontinuityNameMap.size());
        for (Discontinuity od : discontinuityNameMap.keySet()) {
            printWriter.println(discontinuityNameMap.get(od) + " " + od.getDiscontinuityExp().flatten().infix() + "; " + od.getRootFindingExp().flatten().infix() + ";");
        }
    }
    if (eventString != null) {
        printWriter.print(eventString);
    }
    printWriter.println("NUM_EQUATIONS " + getStateVariableCount());
    printWriter.println(equationString);
}