// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2024.
   //
   // This file is part of Force Field X.
   //
   // Force Field X is free software; you can redistribute it and/or modify it
  // under the terms of the GNU General Public License version 3 as published by
  // the Free Software Foundation.
  //
  // Force Field X is distributed in the hope that it will be useful, but WITHOUT
  // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
  // details.
  //
  // You should have received a copy of the GNU General Public License along with
  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
  //
  // Linking this library statically or dynamically with other modules is making a
  // combined work based on this library. Thus, the terms and conditions of the
  // GNU General Public License cover the whole combination.
  //
  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
  // executable, regardless of the license terms of these independent modules, and
  // to copy and distribute the resulting executable under terms of your choice,
  // provided that you also meet, for each linked independent module, the terms
  // and conditions of the license of that module. An independent module is a
  // module which is not derived from or based on this library. If you modify this
  // library, you may extend this exception to your version of the library, but
  // you are not obligated to do so. If you do not wish to do so, delete this
  // exception statement from your version.
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  // ******************************************************************************
  package ffx.algorithms.thermodynamics;
  
  import ffx.utilities.FileUtils;
  import ffx.utilities.HistogramXmlAdapter;
  import jakarta.xml.bind.JAXBContext;
  import jakarta.xml.bind.Marshaller;
  import jakarta.xml.bind.Unmarshaller;
  import jakarta.xml.bind.annotation.XmlAccessOrder;
  import jakarta.xml.bind.annotation.XmlAccessType;
  import jakarta.xml.bind.annotation.XmlAccessorOrder;
  import jakarta.xml.bind.annotation.XmlAccessorType;
  import jakarta.xml.bind.annotation.XmlElement;
  import jakarta.xml.bind.annotation.XmlRootElement;
  import jakarta.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
  import org.apache.commons.configuration2.CompositeConfiguration;
  
  import javax.annotation.Nullable;
  import java.io.File;
  import java.util.logging.Logger;
  
  import static java.lang.Math.pow;
  import static java.lang.Math.round;
  import static java.lang.String.format;
  
  @XmlRootElement(name = "HistogramData")
  @XmlAccessorOrder(XmlAccessOrder.ALPHABETICAL)
  @XmlAccessorType(XmlAccessType.NONE)
  public class HistogramData {
  
    private static final Logger logger = Logger.getLogger(HistogramData.class.getName());
  
    /**
     * The default Gaussian bias magnitude is 0.05 kcal/mol.
     */
    private static final double DEFAULT_BIAS_MAG = 0.05;
  
    /**
     * The default dU/dL bias cutoff is 5 bins.
     */
    private static final int DEFAULT_DUDL_BIAS_CUTOFF = 5;
  
    /**
     * The default lambda bias cutoff is 5 bins for continuous lambda and 0 bins for discrete lambda.
     */
    private static final int DEFAULT_LAMBDA_BIAS_CUTOFF = 5;
  
    /**
     * The default count interval is 10 MD steps.
     */
    private static final int DEFAULT_COUNT_INTERVAL = 10;
  
    /**
     * The default lambda bin width is 0.005.
     * There are (1.0 / width - 1) full size bins (e.g., 199 for width = 0.005).
     * The first and last bins are half size (e.g., 0.0025 for width = 0.005).
     */
    private static final double DEFAULT_LAMBDA_BIN_WIDTH = 0.005;
  
    /**
     * The default number of lambda bins is 201 based on DEFAULT_LAMBDA_BIN_WIDTH = 0.005.
     * The first and last bin are of size DEFAULT_LAMBDA_BIN_WIDTH / 2.
     * Bin 0:   0.0 to DEFAULT_LAMBDA_BIN_WIDTH / 2.
    * Bin 200: 1.0 - DEFAULT_LAMBDA_BIN_WIDTH / 2 to 1.0.
    * Bins 1 to 199 have size DEFAULT_LAMBDA_BIN_WIDTH.
    */
   private static final int DEFAULT_LAMBDA_BINS = 201;
 
   /**
    * The default dU/dL bin width is 2.0 kcal/mol.
    */
   private static final double DEFAULT_DUDL_BIN_WIDTH = 2.0;
 
   /**
    * Default number of dU/dL bins is 101.
    */
   private static final int DEFAULT_DUDL_BINS = 101;
 
   /**
    * The default dU/dL range is from -DEFAULT_DUDL_BINS to DEFAULT_DUDL_BINS.
    * This depends on the 1) default bin width of 2.0 kcal/mol and 2) the central bin range of -1.0 to 1.0.
    * The default dU/dL minimum is -101 kcal/mol and the maximum is 101 kcal/mol.
    */
   private static final double DEFAULT_DUDL_MINIMUM = -DEFAULT_DUDL_BINS;
 
   /**
    * Default is that meta-dynamics is not used.
    */
   private static final boolean DEFAULT_METADYNAMICS = false;
 
   /**
    * The default tempering factor is 2.0 (in units of kBT).
    */
   private static final double DEFAULT_TEMPERING_FACTOR = 2.0;
 
   /**
    * The default lambda reset value is at lambda = 0.99.
    */
   private static final double DEFAULT_RESET_HISTOGRAM_AT_LAMBDA = 0.99;
 
   /**
    * The default reset statistics flag is false.
    */
   private static final boolean DEFAULT_RESET_HISTOGRAM = false;
 
   /**
    * The default tempering offset is DEFAULT_BIAS_TO_TEMPERING_OFFSET * DEFAULT_BIAS_MAG = 1.0 kcal/mol.
    */
   private final double DEFAULT_BIAS_TO_TEMPERING_OFFSET = 20.0;
 
   /**
    * By default, each walker contributes to the same histogram.
    */
   private final boolean DEFAULT_INDEPENDENT_WALKERS = false;
 
   /**
    * By default, only the Rank 0 process writes the histogram.
    * <p>
    * Note that if independent walkers are used, each walker will write its own histogram.
    */
   private final boolean DEFAULT_INDEPENDENT_WRITE = false;
 
   /**
    * By default, the lambda state variable is continuous. If discreteLambda is true, the lambda state is discrete.
    */
   private static final boolean DEFAULT_DISCRETE_LAMBDA = false;
 
   /**
    * Magnitude of each hill (not including tempering). The default biasMag = 0.05 (kcal/mol).
    */
   @XmlElement(name = "BiasMag", defaultValue = "" + DEFAULT_BIAS_MAG)
   double biasMag = DEFAULT_BIAS_MAG;
 
   /**
    * When evaluating the biasing potential, contributions from a Gaussian centered on a bin more
    * than lambdaBiasCutoff away will be neglected.
    * The continuous lambda simulations, the default lambdaBiasCutoff = 5.
    * For discrete lambda simulations, the default lambdaBiasCutoff = 0.
    */
   @XmlElement(name = "LambdaBiasCutoff", defaultValue = "" + DEFAULT_LAMBDA_BIAS_CUTOFF)
   int lambdaBiasCutoff = DEFAULT_LAMBDA_BIAS_CUTOFF;
 
   /**
    * When evaluating the biasing potential, contributions from a Gaussian centered on a bin more
    * than dUdLBiasCutoff" away will be neglected. The default dUdLBiasCutoff = 5.
    */
   @XmlElement(name = "dUdLBiasCutoff", defaultValue = "" + DEFAULT_DUDL_BIAS_CUTOFF)
   int dUdLBiasCutoff = DEFAULT_DUDL_BIAS_CUTOFF;
 
   /**
    * Interval between adding a count to the Recursion kernel in MD steps. The default countInterval = 10.
    */
   @XmlElement(name = "CountInterval", defaultValue = "" + DEFAULT_COUNT_INTERVAL)
   int countInterval = DEFAULT_COUNT_INTERVAL;
 
   /**
    * Width of a lambda bin, or the distance between discrete lambda values.
    * The default is 1.0 / (lambdaBins - 1).
    */
   @XmlElement(name = "LambdaBinWidth", defaultValue = "" + DEFAULT_LAMBDA_BIN_WIDTH)
   double lambdaBinWidth = DEFAULT_LAMBDA_BIN_WIDTH;
 
   /**
    * If true, use discrete lambda values instead of continuous lambda values.
    */
   @XmlElement(name = "DiscreteLambda", defaultValue = "" + DEFAULT_DISCRETE_LAMBDA)
   boolean discreteLambda = DEFAULT_DISCRETE_LAMBDA;
 
   /**
    * The width of the FLambda bin. The default is 2.0 (kcal/mol).
    */
   @XmlElement(name = "dUdLBinWidth", defaultValue = "" + DEFAULT_DUDL_BIN_WIDTH)
   double dUdLBinWidth = DEFAULT_DUDL_BIN_WIDTH;
 
   /**
    * The minimum value of the first dU/dL bin.
    * Initially this is set to: mindUdL = -(dUdLBinWidth * dUdLBins) / 2.0.
    * However, mindUdL may be updated as the count matrix is dynamically resized.
    */
   @XmlElement(name = "dUdLMinimum", defaultValue = "" + DEFAULT_DUDL_MINIMUM)
   double dUdLMinimum = DEFAULT_DUDL_MINIMUM;
 
   /**
    * Flag to indicate use of 1D meta-dynamics instead of OST.
    */
   @XmlElement(name = "MetaDynamics", defaultValue = "" + DEFAULT_METADYNAMICS)
   boolean metaDynamics = DEFAULT_METADYNAMICS;
 
   /**
    * The Dama et al. transition-tempering rate parameter. A reasonable value is about 2 to 8 kT,
    * with larger values being resulting in slower decay. The default temperingFactor = 2.0.
    */
   @XmlElement(name = "TemperingFactor", defaultValue = "" + DEFAULT_TEMPERING_FACTOR)
   double temperingFactor = DEFAULT_TEMPERING_FACTOR;
 
   /**
    * An offset applied before calculating tempering weight.
    * <p>
    * First, for every Lambda, we calculate the maximum bias at that lambda by searching all
    * populated dU/dL bins: maxdUdL(L) = max[ G(L,F_L) ] where the max operator searches over all F_L
    * bins.
    * <p>
    * Then, the minimum bias coverage is determined by searching the maxdUdL(L) array over Lambda.
    * minBias = min[ maxdUdL(L) ] where the min operator searches all entries in the array.
    * <p>
    * Then the temperOffset is applied to the minBias: biasHeight = max[minBias - temperingOffset, 0]
    * <p>
    * The default temperingOffset = 20x the Gaussian bias magnitude.
    */
   @XmlElement(name = "TemperingOffset", defaultValue = "-1.0")
   private double temperingOffset = -1.0;
 
   /**
    * Once the lambda reset value is reached, OST statistics are reset.
    */
   @XmlElement(name = "ResetHistogramAtLambda", defaultValue = "" + DEFAULT_RESET_HISTOGRAM_AT_LAMBDA)
   double resetHistogramAtLambda = DEFAULT_RESET_HISTOGRAM_AT_LAMBDA;
 
   /**
    * Flag set to false once OST statistics are reset at lambdaResetValue.
    */
   @XmlElement(name = "ResetHistogram", defaultValue = "" + DEFAULT_RESET_HISTOGRAM)
   boolean resetHistogram = DEFAULT_RESET_HISTOGRAM;
 
   @XmlElement(name = "IndependentWalkers", defaultValue = "" + DEFAULT_INDEPENDENT_WALKERS)
   boolean independentWalkers = DEFAULT_INDEPENDENT_WALKERS;
 
   @XmlElement(name = "IndependentWrite", defaultValue = "" + DEFAULT_INDEPENDENT_WRITE)
   boolean independentWrite = DEFAULT_INDEPENDENT_WRITE;
 
   /**
    * Flag to indicate if OST should send and receive counts between processes synchronously or
    * asynchronously. The latter can be faster by ~40% because simulation with Lambda &gt; 0.75 must
    * compute two condensed phase self-consistent fields to interpolate polarization.
    */
   @XmlElement(name = "Asynchronous", defaultValue = "" + true)
   boolean asynchronous = true;
 
   /**
    * It is useful to have an odd number of bins, so that there is a bin from FL=-dFL/2 to dFL/2 so
    * that as FL approaches zero its contribution to thermodynamic integration goes to zero.
    * <p>
    * Otherwise a contribution of zero from a L bin can only result from equal sampling of the
    * ranges -dFL to 0 and 0 to dFL.
    * <p>
    * The default FLambdaBins = 101.
    */
   @XmlElement(name = "dUdLBins", defaultValue = "" + DEFAULT_DUDL_BINS)
   public int dUdLBins = DEFAULT_DUDL_BINS;
 
   /**
    * The number of hills added to the recursion kernel.
    */
   @XmlElement(name = "Counts", defaultValue = "0")
   public int counts = 0;
 
   /**
    * The recursion kernel stores the weight of each [lambda][dU/dL] bin.
    * Note that the variable name begins with Z so that its last in the histogram XML file.
    */
   @XmlElement(name = "Data", required = true)
   @XmlJavaTypeAdapter(HistogramXmlAdapter.class)
   double[][] zHistogram = new double[DEFAULT_LAMBDA_BINS][DEFAULT_DUDL_BINS];
 
   /**
    * The histogram file to write to / read from.
    */
   private File histogramFile = null;
 
   /**
    * The name of the histogram file.
    */
   private String histogramFileName = null;
 
   /**
    * Flag indicating if this histogram data came from reading a file.
    */
   private boolean histogramRead = false;
 
   /**
    * For continuous lambda: The first Lambda bin is centered on 0.0 (-0.0025 to 0.0025). The final
    * Lambda bin is centered on 1.0 ( 0.9975 to 1.0025).
    * <p>
    * With this scheme, the maximum of biasing Gaussian hills is at exactly 0.0 and 1.0.
    * <p>
    * For discrete lambda: The first value of lambda is 0.0 and last value is 1.0.
    * <p>
    * The default lambdaBins = 201.
    */
   public int lambdaBins = DEFAULT_LAMBDA_BINS;
 
   /**
    * Half the width of a lambda bin, or zero for discrete lambda values.
    */
   public double lambdaBinWidth_2 = DEFAULT_LAMBDA_BIN_WIDTH / 2.0;
 
   /**
    * The minimum value of the first lambda bin.
    * <p>
    * minLambda = -dL_2 for continuous lambda.
    * <p>
    * minLambda = 0 for discrete lambda.
    */
   public double minLambda = -DEFAULT_LAMBDA_BIN_WIDTH / 2.0;
 
   /**
    * Either the discrete lambda values used, or null (continuous lambda).
    */
   public double[] lambdaLadder = null;
 
   /**
    * The variance for the Gaussian bias in the lambda dimension.
    * lambdaVariance = 2.0 * dL * 2.0 * dL;
    */
   public double lambdaVariance = pow(2.0 * DEFAULT_LAMBDA_BIN_WIDTH, 2);
 
 
   /**
    * The maximum value of the last dUdL bin.
    * <p>
    * maxdUdL = mindUdL + dUdLBins * dUdLBinWidth.
    * <p>
    * default = -101 + 101 * 2.0 = 101 = DEFAULT_DUDL_BINS.
    */
   public double dUdLMaximum = DEFAULT_DUDL_BINS;
 
   /**
    * Half the width of the F_lambda bin.
    */
   public double dUdLBinWidth_2 = DEFAULT_DUDL_BIN_WIDTH / 2.0;
 
   /**
    * The variance for the Gaussian bias in the dU/dL dimension.
    * dUdLVariance = 2.0 * dFL * 2.0 * dFL;
    */
   public double dUdLVariance = pow(2.0 * dUdLBinWidth, 2);
 
   /**
    * Marshall the histogram data to a file.
    *
    * @param histogramData The Histogram data.
    * @param file          The file to write to.
    */
   public static void writeHistogram(HistogramData histogramData, File file) {
     try {
       JAXBContext jaxbContext = JAXBContext.newInstance(HistogramData.class);
       Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
       jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
       jaxbMarshaller.marshal(histogramData, file);
     } catch (Exception e) {
       logger.warning(" Exception writing histogram:\n " + e);
     }
   }
 
   /**
    * Unmarshall the histogram data.
    *
    * @param file The file to read from.
    * @return The Histogram data.
    */
   public static HistogramData readHistogram(@Nullable File file) {
     if (file != null && file.exists() && file.canRead()) {
       try {
         JAXBContext jaxbContext = JAXBContext.newInstance(HistogramData.class);
         Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
         HistogramData histogramData = (HistogramData) unmarshaller.unmarshal(file);
         histogramData.setHistogramFile(file);
         histogramData.setHistogramRead(true);
         histogramData.rectify();
         return histogramData;
       } catch (Exception e) {
         logger.warning(" Exception reading histogram:\n " + e);
       }
     }
     HistogramData histogramData = new HistogramData();
     histogramData.setHistogramFile(file);
     histogramData.rectify();
     return histogramData;
   }
 
   private void rectify() {
     // Check that histogram size matches the number of lambda and dU/dL bins.
     int hisLambdaBins = zHistogram.length;
     if (lambdaBins != hisLambdaBins) {
       logger.fine(" Current LambdaBins: " + lambdaBins);
       logger.fine(" Updated to:         " + hisLambdaBins);
       lambdaBins = hisLambdaBins;
       lambdaBinWidth = 1.0 / (lambdaBins - 1);
     }
     int hisDUDLBins = zHistogram[0].length;
     if (dUdLBins != hisDUDLBins) {
       logger.fine(" Current dUdLBins:   " + dUdLBins);
       logger.fine(" Updated to:         " + hisDUDLBins);
       dUdLBins = hisDUDLBins;
     }
     rectifyLambdaVariables();
     rectifyDUDLVariables();
   }
 
   /**
    * All transient variables that depend on dUdLBinWidth are set here.
    */
   private void rectifyDUDLVariables() {
     // The center of the central bin is at 0.
     dUdLBinWidth_2 = dUdLBinWidth / 2.0;
     dUdLMaximum = dUdLMinimum + (dUdLBins * dUdLBinWidth);
     dUdLVariance = pow(2.0 * dUdLBinWidth, 2);
   }
 
   /**
    * All transient variables that depend on lambdaBinWidth or discreteLambda are set here.
    */
   private void rectifyLambdaVariables() {
     // Get the closest number of full width bins based on the current lambdaBinWidth.
     int n = (int) round(1.0 / lambdaBinWidth);
     // Now set the lambdaBinWidth exactly.
     lambdaBinWidth = 1.0 / n;
     // Divide a bin into two half size bins (the first and last bins are centered on 0 and 1, respectively).
     lambdaBins = n + 1;
     if (discreteLambda) {
       lambdaLadder = new double[lambdaBins];
       lambdaLadder[0] = 0.0;
       lambdaLadder[lambdaBins - 1] = 1.0;
       for (int i = 1; i < lambdaBins - 1; i++) {
         lambdaLadder[i] = lambdaBinWidth * i;
       }
       lambdaBinWidth_2 = 0.0;
       minLambda = 0.0;
       lambdaBiasCutoff = 0;
     } else {
       lambdaLadder = null;
       lambdaBinWidth_2 = lambdaBinWidth / 2.0;
       minLambda = -lambdaBinWidth_2;
       // Leave the lambda bias cutoff at it current value, unless its zero.
       if (lambdaBiasCutoff == 0) {
         // In this case, set it back to the default value.
         lambdaBiasCutoff = DEFAULT_LAMBDA_BIAS_CUTOFF;
       }
     }
     lambdaVariance = pow(2.0 * lambdaBinWidth, 2);
   }
 
   public void setCountInterval(int countInterval) {
     this.countInterval = countInterval;
   }
 
   /**
    * Marshall this histogram data to a file.
    */
   public void writeHistogram() {
     writeHistogram(this, histogramFile);
   }
 
   public String getHistogramFileName() {
     return histogramFileName;
   }
 
   public File getHistogramFile() {
     return histogramFile;
   }
 
   public void setHistogramFile(@Nullable File histogramFile) {
     this.histogramFile = histogramFile;
     if (histogramFile != null) {
       histogramFileName = FileUtils.relativePathTo(histogramFile).toString();
     }
   }
 
   public boolean wasHistogramRead() {
     return histogramRead;
   }
 
   public void setHistogramRead(boolean histogramRead) {
     this.histogramRead = histogramRead;
   }
 
   /**
    * Sets the value of independentWalkers; if true, it also sets writeIndependent to true.
    *
    * @param independentWalkers Value to set independentWalkers to.
    */
   public void setIndependentWalkers(boolean independentWalkers) {
     this.independentWalkers = independentWalkers;
     if (independentWalkers) {
       setWriteIndependent(true);
     }
   }
 
   /**
    * Sets the value of writeIndependent.
    *
    * @param independentWrite Value to set writeIndependent to.
    * @throws IllegalArgumentException If independentWrite is false and independentWalkers is true.
    */
   public void setWriteIndependent(boolean independentWrite) throws IllegalArgumentException {
     if (!independentWrite && independentWalkers) {
       throw new IllegalArgumentException(" Independent walkers implies independent writing.");
     }
     this.independentWrite = independentWrite;
   }
 
   /**
    * Returns the value of independentWrite.
    *
    * @return independentWrite.
    */
   public boolean independentWrite() {
     return independentWrite;
   }
 
   /**
    * Gets the Gaussian bias magnitude in kcal/mol.
    *
    * @return Gaussian bias magnitude in kcal/mol.
    */
   public double getBiasMag() {
     return biasMag;
   }
 
   /**
    * Set the bias magnitude. If temperingOffset has not been explicitly set,
    * the temperOffset is set to bias magnitude * 20.
    *
    * @param biasMag Gaussian bias magnitude in kcal/mol
    */
   public void setBiasMag(double biasMag) {
     this.biasMag = biasMag;
   }
 
   public void setTemperingFactor(double temperingFactor) {
     this.temperingFactor = temperingFactor;
   }
 
   public void setMetaDynamics(boolean metaDynamics) {
     this.metaDynamics = metaDynamics;
   }
 
   public double getLambdaBinWidth() {
     return lambdaBinWidth;
   }
 
   public int getLambdaBins() {
     return lambdaBins;
   }
 
   public int getDUDLBins() {
     return dUdLBins;
   }
 
   /**
    * Sets lambdaBinWidth; if an invalid value is provided (not 0-1), resets it to default 0.005.
    *
    * @param lambdaBinWidth Lambda bin width.
    */
   public void setLambdaBinWidth(double lambdaBinWidth) {
     if (lambdaBinWidth <= 0.0 || lambdaBinWidth > 1.0) {
       this.lambdaBinWidth = DEFAULT_LAMBDA_BIN_WIDTH;
     } else {
       this.lambdaBinWidth = lambdaBinWidth;
     }
     rectifyLambdaVariables();
   }
 
   /**
    * Gets the tempering offset.
    *
    * @return Gets the tempering offset in kcal/mol.
    */
   public double getTemperingOffset() {
     if (temperingOffset >= 0.0) {
       return temperingOffset;
     }
     return biasMag * DEFAULT_BIAS_TO_TEMPERING_OFFSET;
   }
 
   /**
    * Sets an explicit tempering offset in kcal/mol.
    *
    * @param temperingOffset Tempering offset in kcal/mol.
    */
   public void setTemperingOffset(double temperingOffset) {
     this.temperingOffset = temperingOffset;
     this.temperingOffset = temperingOffset;
   }
 
   public void setAsynchronous(boolean asynchronous) {
     this.asynchronous = asynchronous;
   }
 
   public double resetHistogramAtLambda() {
     return resetHistogramAtLambda;
   }
 
   /**
    * Set the lambda value at which to reset the histogram.
    *
    * @param resetHistogramAtLambda The lambda value at which to reset the histogram.
    */
   public void setResetHistogramAtLambda(double resetHistogramAtLambda) {
     if (resetHistogramAtLambda < 0.0 || resetHistogramAtLambda > 1.0) {
       this.resetHistogramAtLambda = DEFAULT_RESET_HISTOGRAM_AT_LAMBDA;
       this.resetHistogram = false;
     } else {
       this.resetHistogramAtLambda = resetHistogramAtLambda;
       this.resetHistogram = true;
     }
   }
 
   public void setDiscreteLambda(boolean discreteLambda) {
     this.discreteLambda = discreteLambda;
     rectifyLambdaVariables();
   }
 
   public void applyProperties(CompositeConfiguration properties) {
     if (properties.containsKey("lambda-bias-cutoff")) {
       lambdaBiasCutoff = properties.getInt("lambda-bias-cutoff");
     }
     if (properties.containsKey("dudl-bias-cutoff")) {
       dUdLBiasCutoff = properties.getInt("dudl-bias-cutoff");
     }
     if (properties.containsKey("ost-bias-mag")) {
       double bias = properties.getDouble("ost-bias-mag");
       setBiasMag(bias);
     }
     if (properties.containsKey("ost-temperOffset")) {
       double offset = properties.getDouble("ost-temperOffset");
       setTemperingOffset(offset);
     }
     if (properties.containsKey("lambda-bin-width")) {
       double width = properties.getDouble("lambda-bin-width");
       setLambdaBinWidth(width);
     }
     if (properties.containsKey("flambda-bin-width")) {
       dUdLBinWidth = properties.getDouble("flambda-bin-width");
     }
     if (properties.containsKey("discrete-lambda")) {
       boolean discreteLambda = properties.getBoolean("discrete-lambda");
       setDiscreteLambda(discreteLambda);
     }
   }
 
   public String toString() {
     return format("  Lambda bins:      %6d\n", lambdaBins)
         + format("  Lambda bin width: %6.3f\n", lambdaBinWidth)
         + format("  dU/dL bins:       %6d\n", dUdLBins)
         + format("  dU/dL bin width:  %6.3f (kcal/mol)\n", dUdLBinWidth)
         + format("  Bias magnitude:   %6.3f (kcal/mol)\n", biasMag)
         + format("  Tempering offset: %6.3f (kcal/mol)\n", getTemperingOffset())
         + format("  Tempering rate:   %6.3f\n", temperingFactor)
         + format("  Discrete lambda:  %6B\n", discreteLambda)
         + format("  Meta-dynamics:    %6B\n\n", metaDynamics);
   }
 
 }