// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2026.
   //
   // This file is part of Force Field X.
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  package ffx.algorithms.cli;
  
  import ffx.algorithms.AlgorithmListener;
  import ffx.algorithms.dynamics.MDEngine;
  import ffx.algorithms.dynamics.MolecularDynamics;
  import ffx.algorithms.thermodynamics.HistogramData;
  import ffx.algorithms.thermodynamics.LambdaData;
  import ffx.algorithms.thermodynamics.MonteCarloOST;
  import ffx.algorithms.thermodynamics.OrthogonalSpaceTempering;
  import ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.OptimizationParameters;
  import ffx.crystal.CrystalPotential;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.bonded.LambdaInterface;
  import ffx.potential.cli.WriteoutOptions;
  import org.apache.commons.configuration2.CompositeConfiguration;
  import org.apache.commons.configuration2.Configuration;
  import picocli.CommandLine.ArgGroup;
  import picocli.CommandLine.Option;
  
  import javax.annotation.Nullable;
  import java.io.File;
  import java.util.logging.Logger;
  
  /**
   * Represents command line options for scripts that utilize variants of the Orthogonal Space
   * Tempering (OST) algorithm. Metadynamics will be treated as a special case of OST where there is no
   * dU/dL axis.
   *
   * @author Michael J. Schnieders
   * @author Jacob M. Litman
   * @since 1.0
   */
  public class OSTOptions {
  
    private static final Logger logger = Logger.getLogger(OSTOptions.class.getName());
  
    /**
     * The ArgGroup keeps the OSTOptionGroup together when printing help.
     */
    @ArgGroup(heading = "%n Orthogonal Space Tempering Options%n", validate = false)
    private final OSTOptionGroup group = new OSTOptionGroup();
  
    /**
     * The ArgGroup keeps the OSTOptionGroup together when printing help.
     */
    @ArgGroup(heading = "%n Monte Carlo Orthogonal Space Tempering Options%n", validate = false)
    private final MCOSTOptionGroup mcGroup = new MCOSTOptionGroup();
  
    /**
     * Applies relevant options to an OST, and returns either the OST object or something that wraps
     * the OST (such as a Barostat).
     *
     * @param orthogonalSpaceTempering Orthogonal Space Tempering.
     * @param firstAssembly            Primary assembly in OST.
     * @param dynamicsOptions          MD options.
     * @param barostatOptions          NPT options.
     * @return a {@link ffx.crystal.CrystalPotential} object.
     */
    public CrystalPotential applyAllOSTOptions(OrthogonalSpaceTempering orthogonalSpaceTempering,
                                               MolecularAssembly firstAssembly, DynamicsOptions dynamicsOptions,
                                               BarostatOptions barostatOptions) {
      if (dynamicsOptions.getOptimize()) {
       OptimizationParameters opt = orthogonalSpaceTempering.getOptimizationParameters();
       opt.setOptimization(true, firstAssembly);
     }
     return barostatOptions.checkNPT(firstAssembly, orthogonalSpaceTempering);
   }
 
   /**
    * Runs MC-OST.
    *
    * @param monteCarloOST         MC-OST to run.
    * @param dynamicsOptions       Dynamics options.
    * @param thermodynamicsOptions Thermodynamics options.
    */
   public void beginMCOST(MonteCarloOST monteCarloOST, DynamicsOptions dynamicsOptions,
                          ThermodynamicsOptions thermodynamicsOptions) {
     long nEquil = thermodynamicsOptions.getEquilSteps();
 
     if (nEquil > 0) {
       logger.info("\n Beginning MC-OST equilibration.");
       monteCarloOST.setTotalSteps(nEquil);
       if (mcGroup.twoStep) {
         monteCarloOST.sampleTwoStep();
       } else {
         monteCarloOST.sampleOneStep();
       }
       monteCarloOST.setEquilibration(false);
       logger.info("\n Finished MC-OST equilibration.");
     }
 
     logger.info("\n Beginning MC-OST sampling.");
     monteCarloOST.setLambdaStdDev(mcGroup.mcLambdaStdDev);
     monteCarloOST.setTotalSteps(dynamicsOptions.getSteps());
 
     if (mcGroup.twoStep) {
       monteCarloOST.sampleTwoStep();
     } else {
       monteCarloOST.sampleOneStep();
     }
   }
 
   /**
    * Assembles a MolecularDynamics wrapped around a Potential.
    *
    * @param molecularAssemblies MolecularAssembly[]
    * @param crystalPotential    Potential to run on
    * @param dynamicsOptions     DynamicsOptions
    * @param algorithmListener   AlgorithmListener
    * @return MolecularDynamics
    */
   public MolecularDynamics assembleMolecularDynamics(MolecularAssembly[] molecularAssemblies,
                                                      CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions,
                                                      AlgorithmListener algorithmListener) {
     // Create the MolecularDynamics instance.
     MolecularAssembly firstTop = molecularAssemblies[0];
 
     dynamicsOptions.init();
 
     MolecularDynamics molDyn = MolecularDynamics.dynamicsFactory(firstTop, crystalPotential,
         algorithmListener, dynamicsOptions.thermostat, dynamicsOptions.integrator, MDEngine.FFX);
     for (int i = 1; i < molecularAssemblies.length; i++) {
       molDyn.addAssembly(molecularAssemblies[i]);
     }
     molDyn.setRestartFrequency(dynamicsOptions.getCheckpoint());
 
     return molDyn;
   }
 
   /**
    * constructOST.
    *
    * @param crystalPotential      a {@link ffx.crystal.CrystalPotential} to build the OST around.
    * @param lambdaRestartFile     a {@link java.io.File} lambda restart file.
    * @param histogramRestartFile  a {@link java.io.File} histogram restart file.
    * @param firstAssembly         the first {@link ffx.potential.MolecularAssembly} in the OST system.
    * @param addedProperties       a {@link org.apache.commons.configuration2.Configuration} with additional properties.
    * @param dynamicsOptions       a {@link ffx.algorithms.cli.DynamicsOptions} with MD-related settings.
    * @param thermodynamicsOptions a {@link ffx.algorithms.cli.ThermodynamicsOptions} with thermodynamics-related settings.
    * @param lambdaParticleOptions a {@link ffx.algorithms.cli.LambdaParticleOptions} with lambda particle-related settings.
    * @param algorithmListener     any {@link ffx.algorithms.AlgorithmListener} that OST should update.
    * @param async                 If OST should use asynchronous communications.
    * @return the newly built {@link OrthogonalSpaceTempering} object.
    */
   public OrthogonalSpaceTempering constructOST(CrystalPotential crystalPotential,
                                                @Nullable File lambdaRestartFile,
                                                File histogramRestartFile, MolecularAssembly firstAssembly,
                                                @Nullable Configuration addedProperties,
                                                DynamicsOptions dynamicsOptions, ThermodynamicsOptions thermodynamicsOptions,
                                                LambdaParticleOptions lambdaParticleOptions,
                                                @Nullable AlgorithmListener algorithmListener, boolean async) {
 
     LambdaInterface lambdaInterface = (LambdaInterface) crystalPotential;
     CompositeConfiguration compositeConfiguration = new CompositeConfiguration(firstAssembly.getProperties());
     if (addedProperties != null) {
       compositeConfiguration.addConfiguration(addedProperties);
     }
 
     // Load HistogramData
     HistogramData histogramData = HistogramData.readHistogram(histogramRestartFile);
     // Apply command line settings to the HistogramData if a restart file wasn't read in.
     int histogramIndex = 0;
     if (histogramData.wasHistogramRead()) {
       logger.info("\n Read histogram restart from: " + histogramRestartFile);
       logger.info(histogramData.toString());
     } else {
       // Overwrite defaults with properties.
       histogramData.applyProperties(compositeConfiguration);
       // Overwrite defaults & properties with command line options.
       histogramData.setIndependentWalkers(group.independentWalkers);
       histogramData.setWriteIndependent(group.independentWalkers);
       histogramData.setAsynchronous(async);
       histogramData.setTemperingFactor(getTemperingParameter(histogramIndex));
       if (thresholdsSet()) {
         histogramData.setTemperingOffset(getTemperingThreshold(histogramIndex));
       }
       histogramData.setMetaDynamics(group.metaDynamics);
       histogramData.setBiasMag(getBiasMag(histogramIndex));
       histogramData.setCountInterval(group.countInterval);
       logger.info("\n OST Histogram Settings");
       logger.info(histogramData.toString());
     }
 
     // Load LambdaData
     if (lambdaRestartFile == null) {
       String filename = histogramRestartFile.toString().replaceFirst("\\.his$", ".lam");
       lambdaRestartFile = new File(filename);
     }
     LambdaData lambdaData = LambdaData.readLambdaData(lambdaRestartFile);
     // Apply command line settings the LambdaData instances.
     if (lambdaData.wasLambdaRead()) {
       logger.info(" Read lambda restart from:    " + lambdaRestartFile);
     } else {
       lambdaData.setHistogramIndex(histogramIndex);
       if (thermodynamicsOptions.getResetNumSteps()) {
         lambdaData.setStepsTaken(0);
       }
     }
 
     OrthogonalSpaceTempering orthogonalSpaceTempering = new OrthogonalSpaceTempering(lambdaInterface,
         crystalPotential, histogramData, lambdaData, compositeConfiguration,
         dynamicsOptions, lambdaParticleOptions, algorithmListener);
     orthogonalSpaceTempering.setHardWallConstraint(mcGroup.mcHardWall);
 
     // Do NOT run applyOSTOptions here, because that can mutate the OST to a Barostat.
     return orthogonalSpaceTempering;
   }
 
   /**
    * Begins MD-OST sampling from an assembled OST.
    *
    * @param orthogonalSpaceTempering The OST object.
    * @param molecularAssemblies      All MolecularAssemblies.
    * @param crystalPotential         The top-layer CrystalPotential.
    * @param dynamicsOptions          Dynamics options.
    * @param writeoutOptions          a {@link WriteoutOptions} object.
    * @param thermodynamicsOptions    Thermodynamics options.
    * @param dynFile                  The .dyn dynamics restart file.
    * @param algorithmListener        AlgorithmListener
    */
   public void beginMDOST(OrthogonalSpaceTempering orthogonalSpaceTempering,
                          MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential,
                          DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions,
                          ThermodynamicsOptions thermodynamicsOptions, File dynFile,
                          AlgorithmListener algorithmListener) {
 
     dynamicsOptions.init();
 
     MolecularDynamics molDyn = assembleMolecularDynamics(molecularAssemblies, crystalPotential,
         dynamicsOptions, algorithmListener);
 
     boolean initVelocities = true;
     long nSteps = dynamicsOptions.getSteps();
     // Start sampling.
     long nEquil = thermodynamicsOptions.getEquilSteps();
     if (nEquil > 0) {
       logger.info("\n Beginning equilibration");
       orthogonalSpaceTempering.setPropagateLambda(false);
       runDynamics(molDyn, nEquil, dynamicsOptions, writeoutOptions, true, dynFile);
       logger.info(" Beginning OST sampling");
       orthogonalSpaceTempering.setPropagateLambda(true);
     } else {
       logger.info(" Beginning OST sampling without equilibration");
       if (!thermodynamicsOptions.getResetNumSteps()) {
         long nEnergyCount = orthogonalSpaceTempering.getEnergyCount();
         if (nEnergyCount > 0) {
           nSteps -= nEnergyCount;
           logger.info(String.format(" Lambda file: %12d steps picked up, now sampling %12d steps",
               nEnergyCount, nSteps));
           initVelocities = false;
         }
       }
     }
     if (nSteps > 0) {
       runDynamics(molDyn, nSteps, dynamicsOptions, writeoutOptions, initVelocities, dynFile);
     } else {
       logger.info(" No steps remaining for this process!");
     }
   }
 
   /**
    * Checks if independent walkers has been specified.
    *
    * @return Walker independence.
    */
   public boolean getIndependentWalkers() {
     return group.independentWalkers;
   }
 
   /**
    * Checks if the use of the Monte Carlo algorithm has been specified.
    *
    * @return Monte Carlo OST (as opposed to molecular dynamics OST).
    */
   public boolean isMonteCarlo() {
     return mcGroup.monteCarlo;
   }
 
   public void setMonteCarlo(boolean monteCarlo) {
     mcGroup.monteCarlo = monteCarlo;
   }
 
   /**
    * Returns true if the 2-step option is enabled (not guaranteed to also mean that MC is enabled!).
    *
    * @return If --ts is enabled.
    */
   public boolean isTwoStep() {
     return mcGroup.twoStep;
   }
 
   public void setTwoStep(boolean twoStep) {
     mcGroup.twoStep = twoStep;
   }
 
   /**
    * setupMCOST.
    *
    * @param orthogonalSpaceTempering a {@link OrthogonalSpaceTempering} object.
    * @param molecularAssemblies      an array of {@link ffx.potential.MolecularAssembly} objects.
    * @param crystalPotential         a {@link ffx.crystal.CrystalPotential} object.
    * @param dynamicsOptions          a {@link ffx.algorithms.cli.DynamicsOptions} object.
    * @param thermodynamicsOptions    a {@link ffx.algorithms.cli.ThermodynamicsOptions} object.
    * @param verbose                  Whether to print out additional information about MC-OST.
    * @param algorithmListener        An AlgorithmListener
    * @return An assembled MonteCarloOST ready to run.
    */
   public MonteCarloOST setupMCOST(OrthogonalSpaceTempering orthogonalSpaceTempering,
                                   MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential,
                                   DynamicsOptions dynamicsOptions,
                                   ThermodynamicsOptions thermodynamicsOptions, boolean verbose,
                                   File dynRestart, AlgorithmListener algorithmListener) {
     dynamicsOptions.init();
 
     MonteCarloOST monteCarloOST = new MonteCarloOST(crystalPotential, orthogonalSpaceTempering,
         molecularAssemblies[0], molecularAssemblies[0].getProperties(),
         algorithmListener, dynamicsOptions, verbose, mcGroup.mcMDSteps, dynRestart);
 
     MolecularDynamics md = monteCarloOST.getMD();
     for (int i = 1; i < molecularAssemblies.length; i++) {
       md.addAssembly(molecularAssemblies[i]);
     }
 
     long nEquil = thermodynamicsOptions.getEquilSteps();
     if (nEquil > 0) {
       monteCarloOST.setEquilibration(true);
     }
     return monteCarloOST;
   }
 
   private boolean thresholdsSet() {
     return group.temperingThreshold.length != 1 || group.temperingThreshold[0] >= 0;
   }
 
   /**
    * Returns the initial bias magnitude associated with a walker.
    *
    * @param i Index of a walker
    * @return Its intended initial bias magnitude in kcal/mol.
    */
   private double getBiasMag(int i) {
     return group.biasMag.length > 1 ? group.biasMag[i] : group.biasMag[0];
   }
 
   private void runDynamics(MolecularDynamics molecularDynamics, long numSteps,
                            DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions, boolean initVelocities,
                            File dyn) {
     molecularDynamics.dynamic(numSteps, dynamicsOptions.getDt(), dynamicsOptions.getReport(),
         dynamicsOptions.getWrite(), dynamicsOptions.getTemperature(), initVelocities,
         writeoutOptions.getFileType(), dynamicsOptions.getCheckpoint(), dyn);
   }
 
   /**
    * Returns the tempering threshold associated with a walker.
    *
    * @param i Index of a walker
    * @return Its intended tempering threshold in kcal/mol.
    */
   private double getTemperingThreshold(int i) {
     return group.temperingThreshold.length > 1 ? group.temperingThreshold[i]
         : group.temperingThreshold[0];
   }
 
   /**
    * Returns the tempering parameter associated with a walker.
    *
    * @param i Index of a walker
    * @return Its intended tempering parameter in kBT.
    */
   private double getTemperingParameter(int i) {
     return group.temperingRate.length > 1 ? group.temperingRate[i] : group.temperingRate[0];
   }
 
   /**
    * Sets the number of time steps between OST counts.
    *
    * @return Returns the interval between OST counts.
    */
   public int getCountInterval() {
     return group.countInterval;
   }
 
   public void setCountInterval(int countInterval) {
     group.countInterval = countInterval;
   }
 
   /**
    * Sets the initial Gaussian bias magnitude in kcal/mol.
    *
    * @return Returns the Bias magnitude.
    */
   public double[] getBiasMag() {
     return group.biasMag;
   }
 
   public void setBiasMag(double[] biasMag) {
     group.biasMag = biasMag;
   }
 
   /**
    * Enforces that each walker maintains their own histogram.
    *
    * @return Returns true if each Walker has their own histogram.
    */
   public boolean isIndependentWalkers() {
     return group.independentWalkers;
   }
 
   public void setIndependentWalkers(boolean independentWalkers) {
     group.independentWalkers = independentWalkers;
   }
 
   /**
    * Use a MetaDynamics style bias.
    *
    * @return Returns true if each Walker has their own histogram.
    */
   public boolean isMetaDynamics() {
     return group.metaDynamics;
   }
 
   public void setMetaDynamics(boolean metaDynamics) {
     group.metaDynamics = metaDynamics;
   }
 
   /**
    * The Dama et al. tempering rate parameter, in multiples of kBT.
    *
    * @return Returns the tempering rate.
    */
   public double[] getTemperingRate() {
     return group.temperingRate;
   }
 
   public void setTemperingRate(double[] temperingRate) {
     group.temperingRate = temperingRate;
   }
 
   /**
    * The tempering threshold/offset in kcal/mol.
    *
    * @return Returns the tempering threshold.
    */
   public double[] getTemperingThreshold() {
     return group.temperingThreshold;
   }
 
   public void setTemperingThreshold(double[] temperingThreshold) {
     group.temperingThreshold = temperingThreshold;
   }
 
   /**
    * The Monte Carlo scheme can use a hard wall that rejects any sample (Lambda, dU/dL) located in an
    * empty histogram bin.
    *
    * @return Returns true if the MC-OST hard wall constraint is set.
    */
   public boolean isMcHardWall() {
     return mcGroup.mcHardWall;
   }
 
   public void setMcHardWall(boolean mcHardWall) {
     mcGroup.mcHardWall = mcHardWall;
   }
 
   /**
    * The number of steps to take for each MD trajectory for MC-OST.
    *
    * @return Returns the number of MD steps for each MC-OST round.
    */
   public int getMcMDSteps() {
     return mcGroup.mcMDSteps;
   }
 
   public void setMcMDSteps(int mcMDSteps) {
     mcGroup.mcMDSteps = mcMDSteps;
   }
 
   /**
    * The standard deviation for lambda moves.
    *
    * @return Returns the MC lambda trial move standard deviations.
    */
   public double getMcLambdaStdDev() {
     return mcGroup.mcLambdaStdDev;
   }
 
   public void setMcLambdaStdDev(double mcLambdaStdDev) {
     mcGroup.mcLambdaStdDev = mcLambdaStdDev;
   }
 
   /**
    * Only write out snapshots if lambda is greater than the value specified.
    *
    * @return Returns the lambda write-out threshold.
    */
   public double getLambdaWriteOut() {
     return group.lambdaWriteOut;
   }
 
   public void setLambdaWriteOut(double lambdaWriteOut) {
     group.lambdaWriteOut = lambdaWriteOut;
   }
 
   /**
    * Collection of Orthogonal Space Tempering Options.
    */
   private static class OSTOptionGroup {
 
     /**
      * -c or --count Sets the number of time steps between OST counts.
      */
     @Option(names = {"-C", "--count"}, paramLabel = "10", defaultValue = "10",
         description = "Time steps between MD Orthogonal Space counts.")
     private int countInterval = 10;
 
     /**
      * --bM or --biasMag sets the initial Gaussian bias magnitude in kcal/mol.
      */
     @Option(names = {"--bM", "--biasMag"}, paramLabel = "0.05", defaultValue = "0.05", split = ",",
         description = "Orthogonal Space Gaussian bias magnitude (kcal/mol); RepEx OST uses a comma-separated list.")
     private double[] biasMag = {0.05};
 
     /**
      * --iW or --independentWalkers enforces that each walker maintains their own histogram.
      */
     @Option(names = {"--iW", "--independentWalkers"}, defaultValue = "false",
         description = "Enforces that each walker maintains their own histogram.")
     private boolean independentWalkers = false;
 
     /**
      * --meta or --metaDynamics Use a 1D metadynamics bias.
      */
     @Option(names = {"--meta", "--metaDynamics"}, defaultValue = "false",
         description = "Use a 1D metadynamics style bias.")
     private boolean metaDynamics = false;
 
     /**
      * --tp or --temperingRate sets the Dama et al. tempering rate parameter (in multiples of kBT).
      */
     @Option(names = {"--tp", "--temperingRate"}, paramLabel = "4.0", defaultValue = "4.0", split = ",",
         description = "Tempering rate parameter in multiples of kBT; RepEx OST uses a comma-separated list.")
     private double[] temperingRate = {4.0};
 
     /**
      * --tth or --temperingThreshold sets the tempering threshold/offset in kcal/mol.
      */
     @Option(names = {"--tth", "--temperingThreshold"}, paramLabel = "20*bias", defaultValue = "-1", split = ",",
         description = "Tempering threshold in kcal/mol; RepEx OST uses a comma-separated list.")
     private double[] temperingThreshold = {-1.0};
 
     /**
      * --lw or --lambdaWriteOut Only write out snapshots if lambda is greater than the value
      * specified.
      */
     @Option(names = {"--lw", "--lambdaWriteOut"}, paramLabel = "0.0", defaultValue = "0.0",
         description = "Only write out snapshots if lambda is greater than the value specified.")
     private double lambdaWriteOut = 0.0;
   }
 
   /**
    * Collection of Monte Carlo Orthogonal Space Tempering Options.
    */
   private static class MCOSTOptionGroup {
 
     /**
      * --mc or --monteCarlo sets the Monte Carlo scheme for Orthogonal Space Tempering.
      */
     @Option(names = {"--mc", "--monteCarlo"}, defaultValue = "false",
         description = "Specify use of Monte Carlo OST")
     private boolean monteCarlo = false;
 
     /**
      * --mcHW or --mcHardWall sets the Monte Carlo scheme to use a hard wall that rejects any sample
      * (Lambda, dU/dL) located in an empty histogram bin.
      */
     @Option(names = {"--mcHW", "--mcHardWall"}, defaultValue = "false",
         description = "Monte Carlo OST hard wall constraint.")
     private boolean mcHardWall = false;
 
     /**
      * --mcmD or --mcMDSteps Sets the number of steps to take for each MD trajectory for MC-OST.
      */
     @Option(names = {"--mcMD", "--mcMDSteps"}, paramLabel = "100", defaultValue = "100",
         description = "Number of dynamics steps to take for each MD trajectory for Monte Carlo OST")
     private int mcMDSteps = 100;
 
     /**
      * --mcL or --mcLambdaStdDev Sets the standard deviation for lambda moves.
      */
     @Option(names = {"--mcL", "--mcLambdaStdDev"}, paramLabel = "0.01", defaultValue = "0.01",
         description = "Standard deviation for lambda move.")
     private double mcLambdaStdDev = 0.01;
 
     /**
      * --ts or --twoStep MC Orthogonal Space sampling using separate lambda and MD moves.
      */
     @Option(names = {"--ts", "--twoStep"}, defaultValue = "false",
         description = "MC Orthogonal Space sampling using separate lambda and MD moves.")
     private boolean twoStep = false;
   }
 
 }