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

Example 6 with SimulationJob

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

the class NfsimExtensionFilter method writeBioModel.

@Override
public void writeBioModel(DocumentManager documentManager, BioModel bioModel, File exportFile, SimulationContext simulationContext) throws Exception {
    // TODO: get the first thing we find for now, in the future we'll need to modify ChooseFile
    // to only offer the applications / simulations with bngl content
    // This should be done by creating one or more additional Selector values and add the filtering logic to ChooseFile
    SimulationContext[] simContexts = bioModel.getSimulationContexts();
    Simulation selectedSim = simulationContext.getSimulations(0);
    // Simulation selectedSim = (Simulation)hashTable.get("selectedSimulation");
    SimulationTask simTask = new SimulationTask(new SimulationJob(selectedSim, 0, null), 0);
    // a fixed seed will allow us to run reproducible simulations
    long randomSeed = 0;
    // long randomSeed = System.currentTimeMillis();
    NFsimSimulationOptions nfsimSimulationOptions = new NFsimSimulationOptions();
    // we get the data we need from the math description
    boolean bUseLocationMarks = true;
    Element root = NFsimXMLWriter.writeNFsimXML(simTask, randomSeed, nfsimSimulationOptions, bUseLocationMarks);
    Document doc = new Document();
    doc.setRootElement(root);
    XMLOutputter xmlOut = new XMLOutputter();
    String resultString = xmlOut.outputString(doc);
    FileUtils.writeStringToFile(exportFile, resultString);
}

Example 7 with SimulationJob

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

the class SmoldynExtensionFilter method writeBioModel.

@Override
public void writeBioModel(DocumentManager documentManager, BioModel bioModel, File exportFile, SimulationContext ignored) throws Exception {
    Objects.requireNonNull(selectedSim);
    int scanCount = selectedSim.getScanCount();
    if (// has parameter scan
    scanCount > 1) {
        String baseExportFileName = exportFile.getPath().substring(0, exportFile.getPath().indexOf("."));
        for (int i = 0; i < scanCount; i++) {
            SimulationTask simTask = new SimulationTask(new SimulationJob(selectedSim, i, null), 0);
            // Need to export each parameter scan into a separate file
            String newExportFileName = baseExportFileName + "_" + i + SMOLDYN_INPUT_FILE_EXTENSION;
            exportFile = new File(newExportFileName);
            PrintWriter pw = new PrintWriter(exportFile);
            SmoldynFileWriter smf = new SmoldynFileWriter(pw, true, null, simTask, false);
            smf.write();
            pw.close();
        }
    } else if (// regular simulation, no parameter scan
    scanCount == 1) {
        SimulationTask simTask = new SimulationTask(new SimulationJob(selectedSim, 0, null), 0);
        // export the simulation to the selected file
        PrintWriter pw = new PrintWriter(exportFile);
        SmoldynFileWriter smf = new SmoldynFileWriter(pw, true, null, simTask, false);
        smf.write();
        pw.close();
    } else {
        throw new Exception("Simulation scan count is smaller than 1.");
    }
}

Example 8 with SimulationJob

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

the class LocalSolverController method solverStarting.

/**
 * Invoked when the solver begins a calculation.
 * @param event indicates the solver and the event type
 */
public void solverStarting(SolverEvent event) {
    try {
        if (lg.isTraceEnabled())
            lg.trace("LocalSolverController Caught solverStarting(" + event.getSource().toString() + ")");
        if (serialParameterScanJobIndex >= 0) {
            SimulationTask newSimTask = new SimulationTask(new SimulationJob(getSimulationTask().getSimulation(), serialParameterScanJobIndex, getSimulationTask().getSimulationJob().getFieldDataIdentifierSpecs()), getSimulationTask().getTaskID());
            fireWorkerEvent(new WorkerEvent(WorkerEvent.JOB_STARTING, this, newSimTask, hostname, event.getSimulationMessage()));
        } else {
            fireWorkerEvent(new WorkerEvent(WorkerEvent.JOB_STARTING, this, getSimulationTask(), hostname, event.getSimulationMessage()));
        }
    } catch (Throwable e) {
        lg.error(e.getMessage(), e);
    }
}

Example 9 with SimulationJob

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

the class LocalSolverController method solverProgress.

/**
 * Invoked when the solver stores values in the result set.
 * @param event indicates the solver and the event type
 */
public void solverProgress(SolverEvent event) {
    try {
        // don't log progress and data events
        if (System.currentTimeMillis() - timeOfLastProgressMessage > 1000 * getMessagingInterval()) {
            if (serialParameterScanJobIndex >= 0) {
                SimulationTask newSimTask = new SimulationTask(new SimulationJob(getSimulationTask().getSimulation(), serialParameterScanJobIndex, getSimulationTask().getSimulationJob().getFieldDataIdentifierSpecs()), getSimulationTask().getTaskID());
                fireWorkerEvent(new WorkerEvent(WorkerEvent.JOB_PROGRESS, this, newSimTask, hostname, new Double(event.getProgress()), new Double(event.getTimePoint()), event.getSimulationMessage()));
                if (event.getProgress() >= 1) {
                    fireWorkerEvent(new WorkerEvent(WorkerEvent.JOB_COMPLETED, this, newSimTask, hostname, new Double(event.getProgress()), new Double(event.getTimePoint()), SimulationMessage.MESSAGE_JOB_COMPLETED));
                    serialParameterScanJobIndex++;
                }
            } else {
                fireWorkerEvent(new WorkerEvent(WorkerEvent.JOB_PROGRESS, this, getSimulationTask(), hostname, new Double(event.getProgress()), new Double(event.getTimePoint()), event.getSimulationMessage()));
            }
        }
    } catch (Throwable e) {
        lg.error(e.getMessage(), e);
    }
}

Example 10 with SimulationJob

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

the class LocalSolverController method solverFinished.

/**
 * Invoked when the solver finishes a calculation (normal termination).
 * @param event indicates the solver and the event type
 */
public void solverFinished(SolverEvent event) {
    try {
        if (lg.isTraceEnabled())
            lg.trace("LocalSolverController Caught solverFinished(" + event.getSource().toString() + ")");
        SimulationJob simJob = getSimulationTask().getSimulationJob();
        if (serialParameterScanJobIndex >= 0) {
            SimulationTask newSimTask = new SimulationTask(new SimulationJob(simJob.getSimulation(), serialParameterScanJobIndex, simJob.getFieldDataIdentifierSpecs()), getSimulationTask().getTaskID());
            fireWorkerEvent(new WorkerEvent(WorkerEvent.JOB_COMPLETED, this, newSimTask, hostname, new Double(event.getProgress()), new Double(event.getTimePoint()), event.getSimulationMessage()));
        } else {
            fireWorkerEvent(new WorkerEvent(WorkerEvent.JOB_COMPLETED, this, getSimulationTask(), hostname, new Double(event.getProgress()), new Double(event.getTimePoint()), event.getSimulationMessage()));
        }
    } catch (Throwable e) {
        lg.error(e.getMessage(), e);
    }
}