Examples with MathExecutable cbit.vcell.solvers.MathExecutable used on opensource projects

Example 1 with MathExecutable

use of cbit.vcell.solvers.MathExecutable in project vcell by virtualcell.

the class SmoldynSolver method initialize.

/**
 *  This method takes the place of the old runUnsteady()...
 */
protected void initialize() throws SolverException {
    if (lg.isTraceEnabled())
        lg.trace("SmoldynSolver.initialize()");
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INIT);
    writeFunctionsFile();
    // write subdomains file
    try {
        SubdomainInfo.write(new File(getBaseName() + SimDataConstants.SUBDOMAINS_FILE_SUFFIX), simTask.getSimulation().getMathDescription());
    } catch (IOException e1) {
        e1.printStackTrace();
        throw new SolverException(e1.getMessage());
    } catch (MathException e1) {
        e1.printStackTrace();
        throw new SolverException(e1.getMessage());
    }
    String inputFilename = getInputFilename();
    if (lg.isTraceEnabled())
        lg.trace("SmoldynSolver.initialize() baseName = " + getBaseName());
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_INPUT_FILE));
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INPUT_FILE);
    PrintWriter pw = null;
    try {
        pw = new PrintWriter(inputFilename);
        if (SystemUtils.IS_OS_WINDOWS) {
            // 
            // the windows executable is compiled under cygwin (or mingw) and expect Unix style line termination characters.
            // so SmoldynInput file is written with platform default Java convention (different on windows) to a String.
            // Then the string is translated to Unix style before written to the file.
            // smoldyn is particularly sensitive to this issue, other compiled solvers are more tolerant.
            // 
            StringWriter stringWriter = new StringWriter();
            PrintWriter pw2 = new PrintWriter(stringWriter);
            SmoldynFileWriter stFileWriter = new SmoldynFileWriter(pw2, false, getBaseName(), simTask, bMessaging);
            stFileWriter.write();
            String fileContents = stringWriter.getBuffer().toString();
            fileContents = fileContents.replace("\r\n", "\n");
            pw.write(fileContents);
        } else {
            // 
            // for linux or macos, no translation is necessary.
            // 
            SmoldynFileWriter stFileWriter = new SmoldynFileWriter(pw, false, getBaseName(), simTask, bMessaging);
            stFileWriter.write();
        }
    } catch (Exception e) {
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_ABORTED, SimulationMessage.solverAborted("Could not generate input file: " + e.getMessage())));
        e.printStackTrace(System.out);
        throw new SolverException(e.getMessage());
    } finally {
        if (pw != null) {
            pw.close();
        }
    }
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_START));
    // get executable path+name.
    setMathExecutable(new MathExecutable(getMathExecutableCommand(), getSaveDirectory()));
// setMathExecutable(new cbit.vcell.solvers.MathExecutable(executableName + " gibson " + getBaseName() + ".stochInput" + " " + getBaseName() + ".stoch"));
}

Example 2 with MathExecutable

use of cbit.vcell.solvers.MathExecutable in project vcell by virtualcell.

the class CVodeSolverStandalone method initialize.

/**
 *  This method takes the place of the old runUnsteady()...
 */
protected void initialize() throws SolverException {
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INIT);
    super.initialize();
    String inputFilename = getInputFilename();
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_INPUT_FILE));
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INPUT_FILE);
    PrintWriter pw = null;
    try {
        pw = new java.io.PrintWriter(inputFilename);
        CVodeFileWriter cvodeFileWriter = new CVodeFileWriter(pw, simTask, bMessaging);
        cvodeFileWriter.write();
    } catch (Exception e) {
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_ABORTED, SimulationMessage.solverAborted("CVODE solver could not generate input file: " + e.getMessage())));
        e.printStackTrace(System.out);
        throw new SolverException("CVODE solver could not generate input file: " + e.getMessage());
    } finally {
        if (pw != null) {
            pw.close();
        }
    }
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_START));
    setMathExecutable(new MathExecutable(getMathExecutableCommand(), getSaveDirectory()));
}

Example 3 with MathExecutable

use of cbit.vcell.solvers.MathExecutable in project vcell by virtualcell.

the class IDASolverStandalone method initialize.

/**
 *  This method takes the place of the old runUnsteady()...
 */
protected void initialize() throws SolverException {
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INIT);
    super.initialize();
    String inputFilename = getInputFilename();
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_INPUT_FILE));
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INPUT_FILE);
    PrintWriter pw = null;
    try {
        pw = new PrintWriter(inputFilename);
        IDAFileWriter idaFileWriter = new IDAFileWriter(pw, simTask, bMessaging);
        idaFileWriter.write();
    } catch (Exception e) {
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_ABORTED, SimulationMessage.solverAborted("Could not generate input file: " + e.getMessage())));
        e.printStackTrace(System.out);
        throw new SolverException("IDA solver could not generate input file: " + e.getMessage());
    } finally {
        if (pw != null) {
            pw.close();
        }
    }
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_START));
    setMathExecutable(new MathExecutable(getMathExecutableCommand(), getSaveDirectory()));
}

Example 4 with MathExecutable

use of cbit.vcell.solvers.MathExecutable in project vcell by virtualcell.

the class GibsonSolver method initialize.

/**
 *  This method takes the place of the old runUnsteady()...
 */
protected void initialize() throws SolverException {
    if (lg.isTraceEnabled())
        lg.trace("StochSolver.initialize()");
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INIT);
    writeFunctionsFile();
    writeLogFile();
    String inputFilename = getInputFilename();
    if (lg.isTraceEnabled())
        lg.trace("StochSolver.initialize() baseName = " + getBaseName());
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_INPUT_FILE));
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INPUT_FILE);
    PrintWriter pw = null;
    try {
        pw = new PrintWriter(inputFilename);
        StochFileWriter stFileWriter = new StochFileWriter(pw, simTask, bMessaging);
        stFileWriter.write();
    } catch (Exception e) {
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_ABORTED, SimulationMessage.solverAborted("Could not generate input file: " + e.getMessage())));
        e.printStackTrace(System.out);
        throw new SolverException("solver input file exception: " + e.getMessage());
    } finally {
        if (pw != null) {
            pw.close();
        }
    }
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_START));
    // get executable path+name.
    setMathExecutable(new MathExecutable(getMathExecutableCommand(), getSaveDirectory()));
// setMathExecutable(new cbit.vcell.solvers.MathExecutable(executableName + " gibson " + getBaseName() + ".stochInput" + " " + getBaseName() + ".stoch"));
}

Example 5 with MathExecutable

use of cbit.vcell.solvers.MathExecutable in project vcell by virtualcell.

the class HybridSolver method initialize.

/**
 *  This method takes the place of the old runUnsteady()...
 */
protected void initialize() throws SolverException {
    if (lg.isTraceEnabled())
        lg.trace("HybridSolver.initialize()");
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INIT);
    writeFunctionsFile();
    writeLogFile();
    // 
    // file used by precompiled solver.
    String inputFilename = getInputFilename();
    // 
    if (lg.isTraceEnabled())
        lg.trace("HybridSolver.initialize() baseName = " + getBaseName());
    // 
    NetCDFWriter ncWriter = new NetCDFWriter(simTask, inputFilename, bMessaging);
    try {
        ncWriter.initialize();
    } catch (Exception e) {
        setSolverStatus(new cbit.vcell.solver.server.SolverStatus(SolverStatus.SOLVER_ABORTED, SimulationMessage.solverAborted("Could not initialize StochFileWriter...")));
        e.printStackTrace(System.out);
        throw new SolverException("autocode init exception: " + e.getMessage());
    }
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_INPUT_FILE));
    fireSolverStarting(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INPUT_FILE);
    // 
    try {
        ncWriter.writeHybridInputFile();
    } catch (Exception e) {
        setSolverStatus(new SolverStatus(SolverStatus.SOLVER_ABORTED, SimulationMessage.solverAborted("Could not generate input file: " + e.getMessage())));
        e.printStackTrace(System.err);
        throw new SolverException("solver input file exception: " + e.getMessage());
    }
    // 
    // 
    setSolverStatus(new SolverStatus(SolverStatus.SOLVER_RUNNING, SimulationMessage.MESSAGE_SOLVER_RUNNING_START));
    // get executable path+name.
    // Hybrid solver's usage: ProgramName <NetCDF Filename> <epsilon> <lambda> <MSR_Tolerance> <SDE_Tolerance> <SDE_dt> [-R <Random Seed>] [-OV]
    setMathExecutable(new MathExecutable(getMathExecutableCommand(), getSaveDirectory()));
}