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

Example 81 with Simulation

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

the class SimulationListPanel method editSimulation.

/**
 * Comment
 */
private void editSimulation() {
    // this should not be possible to call unless exactly one row is selected, but check anyway
    int[] selectedRows = getScrollPaneTable().getSelectedRows();
    if (selectedRows.length > 0) {
        // make sure something is selected...
        Simulation sim = (Simulation) (ivjSimulationListTableModel1.getValueAt(selectedRows[0]));
        SimulationStatus simStatus = getSimulationWorkspace().getSimulationStatus(sim);
        if (!simStatus.isRunning()) {
            // just the first one if more than one selected...
            SimulationWorkspace.editSimulation(this, getSimulationWorkspace().getSimulationOwner(), sim);
            // need to check if parallel option changed
            refreshButtonsLax();
        }
    }
}

Example 82 with Simulation

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

the class SimulationListPanel method quickRun.

/*
	private void particleView() {
		int row = getScrollPaneTable().getSelectedRow();
		if (row < 0) {
			return;
		}
		Simulation selectedSim = getSimulationListTableModel1().getValueAt(row);
		getSimulationWorkspace().getClientSimManager().runSmoldynParticleView(selectedSim);
	}
	*/
private void quickRun(ViewerType viewerType) {
    int row = getScrollPaneTable().getSelectedRow();
    if (row < 0) {
        return;
    }
    activateConsole();
    Simulation selectedSim = getSimulationListTableModel1().getValueAt(row);
    SolverDescription solverDescription = selectedSim.getSolverTaskDescription().getSolverDescription();
    if (solverDescription.equals(SolverDescription.FiniteVolume)) {
        if (getSimulationWorkspace().getSimulationOwner() instanceof SimulationContext) {
            String option = DialogUtils.showOKCancelWarningDialog(SimulationListPanel.this, "Deprecated Solver", VCellErrorMessages.getSemiFVSolverCompiledSolverDeprecated(selectedSim));
            if (option.equals(SimpleUserMessage.OPTION_CANCEL)) {
                return;
            }
            try {
                selectedSim.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
                selectedSim.setIsDirty(true);
            } catch (PropertyVetoException e) {
                e.printStackTrace();
            }
        }
    }
    getSimulationWorkspace().getClientSimManager().runQuickSimulation(selectedSim, viewerType);
}

Example 83 with Simulation

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

the class SimulationListPanel method runSimulations.

/**
 * Comment
 */
private void runSimulations() {
    final ArrayList<Simulation> simList = new ArrayList<Simulation>();
    int[] selections = getScrollPaneTable().getSelectedRows();
    for (int i = 0; i < selections.length; i++) {
        Simulation sim = (Simulation) (ivjSimulationListTableModel1.getValueAt(selections[i]));
        if (sim.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.FiniteVolume)) {
            if (getSimulationWorkspace().getSimulationOwner() instanceof SimulationContext) {
                String option = DialogUtils.showOKCancelWarningDialog(SimulationListPanel.this, "Deprecated Solver", VCellErrorMessages.getSemiFVSolverCompiledSolverDeprecated(sim));
                if (option.equals(SimpleUserMessage.OPTION_CANCEL)) {
                    return;
                }
                try {
                    sim.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
                    sim.setIsDirty(true);
                } catch (PropertyVetoException e) {
                    e.printStackTrace();
                }
            }
        }
        simList.add(sim);
    }
    if (simList.size() > 0) {
        activateConsole();
        Simulation[] toRun = simList.toArray(new Simulation[0]);
        getSimulationWorkspace().runSimulations(toRun, this);
    }
}

Example 84 with Simulation

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

the class SimulationStatusDetailsPanel method simulationStatusDetailsPanel_SimulationStatusDetails.

/**
 * Comment
 */
public void simulationStatusDetailsPanel_SimulationStatusDetails(cbit.vcell.client.desktop.simulation.SimulationStatusDetails simStatusDetails) {
    if (simStatusDetails == null) {
        return;
    }
    Simulation sim = simStatusDetails.getSimulation();
    getNameTextField().setText(sim.getName());
    getIDTextField().setText("" + (sim.getKey() != null ? sim.getKey().toString() : "") + (sim.getSimulationVersion() != null && sim.getSimulationVersion().getParentSimulationReference() != null ? " (parentSimRef=" + sim.getSimulationVersion().getParentSimulationReference().toString() + ")" : ""));
    getSolverTextField().setText(sim.getSolverTaskDescription().getSolverDescription().getDisplayLabel());
    return;
}

Example 85 with Simulation

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

the class SimulationWorkspace method getExpectedSizeBytes.

/**
 * Insert the method's description here.
 * Creation date: (6/12/2001 10:09:25 AM)
 * @return boolean
 * @param simulation cbit.vcell.solver.Simulation
 */
private static long getExpectedSizeBytes(SimulationSymbolTable simSymbolTable) {
    Simulation simulation = simSymbolTable.getSimulation();
    long numTimepoints;
    if (simulation.getMathDescription().isNonSpatialStoch()) {
        numTimepoints = getEstimatedNumTimePointsForStoch(simSymbolTable);
    } else {
        numTimepoints = getExpectedNumTimePoints(simulation);
    }
    int x, y, z;
    int numVariables = 0;
    if (simulation.isSpatial()) {
        x = simulation.getMeshSpecification().getSamplingSize().getX();
        y = simulation.getMeshSpecification().getSamplingSize().getY();
        z = simulation.getMeshSpecification().getSamplingSize().getZ();
        // 
        // compute number of volume variables only (they are multiplied by x*y*z)
        // 
        numVariables = 0;
        Enumeration<Variable> variables = simulation.getMathDescription().getVariables();
        while (variables.hasMoreElements()) {
            Variable var = variables.nextElement();
            if (var instanceof VolVariable) {
                numVariables++;
            }
        }
    } else {
        x = 1;
        y = 1;
        z = 1;
        numVariables = 0;
        Enumeration<Variable> variables = simulation.getMathDescription().getVariables();
        while (variables.hasMoreElements()) {
            Variable var = variables.nextElement();
            if ((var instanceof VolVariable) || (var instanceof Function)) {
                numVariables++;
            }
        }
    }
    // approximate, don't compute header size since it's negligible whenever we approach quota size anyway...
    // values are actually written as longs
    long expectedSize = numTimepoints * numVariables * x * y * z * 8;
    return expectedSize;
}