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

Example 6 with NFsimSimulationOptions

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

the class XmlReader method getSolverTaskDescription.

/**
 * This method returns a SolverTaskDescription Object from a XML Element.
 * Creation date: (5/22/2001 10:51:23 AM)
 * @return cbit.vcell.solver.SolverTaskDescription
 * @param param org.jdom.Element
 * @param simulation cbit.vcell.solver.Simulation
 */
private SolverTaskDescription getSolverTaskDescription(Element param, Simulation simulation) throws XmlParseException {
    // *** create new SolverTaskDescription ***
    SolverTaskDescription solverTaskDesc = new SolverTaskDescription(simulation);
    // Added July 22nd, 2007, used as condition for stochSimOptions or stochHybridOprtions
    SolverDescription sd = null;
    // Retrieve attributes
    String taskType = param.getAttributeValue(XMLTags.TaskTypeTag);
    int keepEvery = -1;
    int keepAtMost = -1;
    if (param.getAttributeValue(XMLTags.KeepEveryTag) != null) {
        keepEvery = Integer.parseInt(param.getAttributeValue(XMLTags.KeepEveryTag));
        keepAtMost = Integer.parseInt(param.getAttributeValue(XMLTags.KeepAtMostTag));
    }
    boolean useSymJacob = new Boolean(param.getAttributeValue(XMLTags.UseSymbolicJacobianAttrTag)).booleanValue();
    String solverName = param.getAttributeValue(XMLTags.SolverNameTag);
    // get sentivity parameter
    Element sensparamElement = param.getChild(XMLTags.ConstantTag, vcNamespace);
    Constant sensitivityparam = null;
    if (sensparamElement != null) {
        sensitivityparam = getConstant(sensparamElement);
    }
    // set Attributes
    try {
        // set solver
        sd = SolverDescription.fromDatabaseName(solverName);
        if (sd == null) {
            System.err.println("====================================== couldn't find solver description name ==========================================");
        }
        solverTaskDesc.setSolverDescription(sd);
        if (taskType.equalsIgnoreCase(XMLTags.UnsteadyTag)) {
            solverTaskDesc.setTaskType(SolverTaskDescription.TASK_UNSTEADY);
        } else if (taskType.equalsIgnoreCase(XMLTags.SteadyTag)) {
            solverTaskDesc.setTaskType(SolverTaskDescription.TASK_STEADY);
        } else {
            throw new XmlParseException("Unexpected task type: " + taskType);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was fired when setting the taskType: " + taskType, e);
    }
    int numProcessors = parseIntWithDefault(param, XMLTags.NUM_PROCESSORS, 1);
    try {
        solverTaskDesc.setNumProcessors(numProcessors);
        solverTaskDesc.setUseSymbolicJacobian(useSymJacob);
        // get TimeBound
        solverTaskDesc.setTimeBounds(getTimeBounds(param.getChild(XMLTags.TimeBoundTag, vcNamespace)));
        // get TimeStep
        solverTaskDesc.setTimeStep(getTimeStep(param.getChild(XMLTags.TimeStepTag, vcNamespace)));
        // get ErrorTolerance
        solverTaskDesc.setErrorTolerance(getErrorTolerance(param.getChild(XMLTags.ErrorToleranceTag, vcNamespace)));
        // get StochSimOptions
        if (simulation != null && simulation.getMathDescription() != null) {
            if (simulation.getMathDescription().isNonSpatialStoch() && param.getChild(XMLTags.StochSimOptionsTag, vcNamespace) != null) {
                // Amended July 22nd, 2007 to read either stochSimOptions or stochHybridOptions
                solverTaskDesc.setStochOpt(getStochSimOptions(param.getChild(XMLTags.StochSimOptionsTag, vcNamespace)));
                if (sd != null && !sd.equals(SolverDescription.StochGibson)) {
                    solverTaskDesc.setStochHybridOpt(getStochHybridOptions(param.getChild(XMLTags.StochSimOptionsTag, vcNamespace)));
                }
            }
        }
        // get OutputOptions
        if (keepEvery != -1) {
            solverTaskDesc.setOutputTimeSpec(new DefaultOutputTimeSpec(keepEvery, keepAtMost));
        }
        OutputTimeSpec ots = getOutputTimeSpec(param.getChild(XMLTags.OutputOptionsTag, vcNamespace));
        if (ots != null) {
            solverTaskDesc.setOutputTimeSpec(getOutputTimeSpec(param.getChild(XMLTags.OutputOptionsTag, vcNamespace)));
        }
        // set SensitivityParameter
        solverTaskDesc.setSensitivityParameter(sensitivityparam);
        // set StopAtSpatiallyUniform
        Element stopSpatiallyElement = param.getChild(XMLTags.StopAtSpatiallyUniform, vcNamespace);
        if (stopSpatiallyElement != null) {
            Element errTolElement = stopSpatiallyElement.getChild(XMLTags.ErrorToleranceTag, vcNamespace);
            if (errTolElement != null) {
                solverTaskDesc.setStopAtSpatiallyUniformErrorTolerance(getErrorTolerance(errTolElement));
            }
        }
        String runParameterScanSeriallyAttributeValue = param.getAttributeValue(XMLTags.RunParameterScanSerially);
        if (runParameterScanSeriallyAttributeValue != null) {
            solverTaskDesc.setSerialParameterScan(new Boolean(runParameterScanSeriallyAttributeValue).booleanValue());
        }
        Element nfsimSimulationOptionsElement = param.getChild(XMLTags.NFSimSimulationOptions, vcNamespace);
        if (nfsimSimulationOptionsElement != null) {
            NFsimSimulationOptions nfsimSimulationOptions = getNFSimSimulationOptions(nfsimSimulationOptionsElement);
            solverTaskDesc.setNFSimSimulationOptions(nfsimSimulationOptions);
        }
        Element smoldySimulationOptionsElement = param.getChild(XMLTags.SmoldynSimulationOptions, vcNamespace);
        if (smoldySimulationOptionsElement != null) {
            SmoldynSimulationOptions smoldynSimulationOptions = getSmoldySimulationOptions(smoldySimulationOptionsElement);
            solverTaskDesc.setSmoldynSimulationOptions(smoldynSimulationOptions);
        }
        Element sundialsPdeSolverOptionsElement = param.getChild(XMLTags.SundialsSolverOptions, vcNamespace);
        if (sundialsPdeSolverOptionsElement != null) {
            SundialsPdeSolverOptions sundialsPdeSolverOptions = getSundialsPdeSolverOptions(sundialsPdeSolverOptionsElement);
            solverTaskDesc.setSundialsPdeSolverOptions(sundialsPdeSolverOptions);
        }
        Element chomboElement = param.getChild(XMLTags.ChomboSolverSpec, vcNamespace);
        if (chomboElement != null) {
            ChomboSolverSpec chombo = getChomboSolverSpec(solverTaskDesc, chomboElement, simulation.getMathDescription().getGeometry().getDimension());
            solverTaskDesc.setChomboSolverSpec(chombo);
        }
        Element mbElement = param.getChild(XMLTags.MovingBoundarySolverOptionsTag, vcNamespace);
        if (mbElement != null) {
            MovingBoundarySolverOptions mb = getMovingBoundarySolverOptions(solverTaskDesc, mbElement);
            solverTaskDesc.setMovingBoundarySolverOptions(mb);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException(e);
    }
    return solverTaskDesc;
}

Example 7 with NFsimSimulationOptions

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

the class XmlReader method getNFSimSimulationOptions.

private NFsimSimulationOptions getNFSimSimulationOptions(Element nfsimSimulationOptionsElement) throws XmlParseException {
    NFsimSimulationOptions so = new NFsimSimulationOptions();
    String temp = null;
    temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_observableComputationOff, vcNamespace);
    if (temp != null) {
        so.setObservableComputationOff(new Boolean(temp));
    }
    temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_moleculeDistance, vcNamespace);
    if (temp != null) {
        so.setMoleculeDistance(new Integer(temp));
    }
    temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_aggregateBookkeeping, vcNamespace);
    if (temp != null) {
        so.setAggregateBookkeeping(new Boolean(temp));
    }
    temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_maxMoleculesPerType, vcNamespace);
    if (temp != null) {
        so.setMaxMoleculesPerType(new Integer(temp));
    }
    temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_equilibrateTime, vcNamespace);
    if (temp != null) {
        so.setEquilibrateTime(new Integer(temp));
    }
    temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_randomSeed, vcNamespace);
    if (temp != null) {
        so.setRandomSeed(new Integer(temp));
    }
    temp = nfsimSimulationOptionsElement.getChildText(XMLTags.NFSimSimulationOptions_preventIntraBonds, vcNamespace);
    if (temp != null) {
        so.setPreventIntraBonds(new Boolean(temp));
    }
    return so;
}

Example 8 with NFsimSimulationOptions

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

the class NFSimSolver method getMathExecutableCommand.

@Override
protected String[] getMathExecutableCommand() {
    String executableName = null;
    try {
        executableName = SolverUtilities.getExes(SolverDescription.NFSim)[0].getAbsolutePath();
    } catch (IOException e) {
        throw new RuntimeException("failed to get executable for solver " + SolverDescription.NFSim.getDisplayLabel() + ": " + e.getMessage(), e);
    }
    String inputFilename = getInputFilename();
    String outputFilename = getOutputFilename();
    String speciesOutputFilename = getSpeciesOutputFilename();
    NFsimSimulationOptions nfsso = simTask.getSimulation().getSolverTaskDescription().getNFSimSimulationOptions();
    ArrayList<String> adv = new ArrayList<String>();
    boolean observableComputationOff = nfsso.getObservableComputationOff();
    if (observableComputationOff == true) {
        // false is by default, no need to specify
        adv.add("-notf");
    }
    Integer moleculeDistance = nfsso.getMoleculeDistance();
    if (moleculeDistance != null) {
        adv.add("-utl");
        adv.add(moleculeDistance + "");
    }
    boolean aggregateBookkeeping = nfsso.getAggregateBookkeeping();
    if (aggregateBookkeeping == true || simTask.getSimulation().getMathDescription().hasSpeciesObservable()) {
        // false is by default, no need to specify
        adv.add("-cb");
    }
    Integer maxMoleculesPerType = nfsso.getMaxMoleculesPerType();
    if (maxMoleculesPerType != null) {
        adv.add("-gml");
        adv.add(maxMoleculesPerType + "");
    }
    Integer equilibrateTime = nfsso.getEquilibrateTime();
    if (equilibrateTime != null) {
        adv.add("-eq");
        adv.add(equilibrateTime + "");
    }
    boolean preventIntraBonds = nfsso.getPreventIntraBonds();
    if (preventIntraBonds == true) {
        // false is by default, no need to specify
        adv.add("-bscb");
    }
    TimeBounds tb = getSimulationJob().getSimulation().getSolverTaskDescription().getTimeBounds();
    double dtime = tb.getEndingTime() - tb.getStartingTime();
    String timeSpecOption1 = "-oSteps";
    String timeSpecOption2 = "10";
    OutputTimeSpec outputTimeSpec = getSimulationJob().getSimulation().getSolverTaskDescription().getOutputTimeSpec();
    if (outputTimeSpec instanceof DefaultOutputTimeSpec) {
        DefaultOutputTimeSpec dots = (DefaultOutputTimeSpec) outputTimeSpec;
        int steps = dots.getKeepAtMost();
        timeSpecOption1 = "-oSteps";
        timeSpecOption2 = Integer.toString(steps);
    } else if (outputTimeSpec instanceof UniformOutputTimeSpec) {
        UniformOutputTimeSpec dots = (UniformOutputTimeSpec) outputTimeSpec;
        double steps = dtime / dots.getOutputTimeStep();
        timeSpecOption1 = "-oSteps";
        int stepsi = (int) Math.round(steps);
        timeSpecOption2 = Integer.toString(stepsi);
    } else {
        throw new RuntimeException("Unsupported output time spec class");
    }
    String[] baseCommands = { "-xml", inputFilename, "-o", outputFilename, "-sim", Double.toString(dtime), "-ss", speciesOutputFilename };
    ArrayList<String> cmds = new ArrayList<String>();
    cmds.add(executableName);
    Integer seed = nfsso.getRandomSeed();
    if (seed != null) {
        cmds.add("-seed");
        cmds.add(seed.toString());
    } else {
        long randomSeed = System.currentTimeMillis();
        randomSeed = randomSeed + simTask.getSimulationJob().getJobIndex();
        // multiply with a large prime number to spread numbers that are too close and in sequence
        randomSeed = randomSeed * 89611;
        Integer rs = (int) randomSeed;
        String str = rs.toString();
        if (str.startsWith("-")) {
            // NFSim wants a positive integer, for anything else is initializing with 0
            str = str.substring(1);
        }
        cmds.add("-seed");
        cmds.add(str);
    // PrintWriter writer;
    // try {
    // writer = new PrintWriter("c:\\TEMP\\aaa\\" + randomSeed + ".txt", "UTF-8");
    // writer.println(str);
    // writer.close();
    // } catch (FileNotFoundException | UnsupportedEncodingException e) {
    // // Auto-generated catch block
    // e.printStackTrace();
    // }
    }
    cmds.add("-vcell");
    cmds.addAll(new ArrayList<String>(Arrays.asList(baseCommands)));
    cmds.add(timeSpecOption1);
    cmds.add(timeSpecOption2);
    cmds.addAll(adv);
    if (bMessaging) {
        cmds.add("-v");
    }
    return cmds.toArray(new String[cmds.size()]);
}