// ******************************************************************************
   //
   // 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.
  //
  // ******************************************************************************
  package ffx.algorithms.thermodynamics;
  
  import ffx.utilities.FileUtils;
  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 javax.annotation.Nullable;
  import java.io.File;
  import java.util.logging.Logger;
  
  import static org.apache.commons.math3.util.FastMath.asin;
  import static org.apache.commons.math3.util.FastMath.sqrt;
  
  @XmlRootElement(name = "LambdaData")
  @XmlAccessorOrder(XmlAccessOrder.ALPHABETICAL)
  @XmlAccessorType(XmlAccessType.NONE)
  public class LambdaData {
  
    private static final Logger logger = Logger.getLogger(LambdaData.class.getName());
  
    /**
     * State variable lambda ranges from 0.0 .. 1.0.
     */
    @XmlElement(name = "Lambda", defaultValue = "0.0")
    double lambda = 0.0;
  
    /**
     * Velocity of the theta particle.
     */
    @XmlElement(name = "ThetaVelocity", defaultValue = "0.0")
    double thetaVelocity = 0.0;
  
    /**
     * Velocity of the theta particle.
     */
    @XmlElement(name = "ThetaAcceleration", defaultValue = "0.0")
    double thetaAcceleration = 0.0;
  
    /**
     * The number of lambda steps taken by the propagate lambda method.
     */
    @XmlElement(name = "StepsTaken", defaultValue = "0")
    long stepsTaken = 0;
  
    /**
     * Index of the current Histogram.
     */
    @XmlElement(name = "HistogramIndex", defaultValue = "0")
    int histogramIndex = 0;
  
    /**
     * The LambdaData file to write to / read from.
     */
    private File lambdaFile = null;
  
   /**
    * The LambdaData file name.
    */
   private String lambdaFileName = null;
 
   /**
    * Flag indicating if this LambdaData came from reading a file.
    */
   private boolean lambdaRead = false;
 
   /**
    * Map lambda to a periodic variable theta.
    * <code>theta = asin(sqrt(lambda))</code>
    * <code>lambda = sin^2 (theta).</code>
    */
   double theta = 0.0;
 
   private void rectify() {
     theta = asin(sqrt(lambda));
   }
 
   /**
    * Marshall the lambda data to a file.
    *
    * @param lambdaData The LambdaData to write.
    * @param lambdaFile The file to write to.
    */
   public static void writeLambdaData(LambdaData lambdaData, File lambdaFile) {
     try {
       JAXBContext jaxbContext = JAXBContext.newInstance(LambdaData.class);
       Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
       jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
       jaxbMarshaller.marshal(lambdaData, lambdaFile);
     } 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 LambdaData readLambdaData(@Nullable File file) {
     if (file != null && file.exists() && file.canRead()) {
       try {
         JAXBContext jaxbContext = JAXBContext.newInstance(LambdaData.class);
         Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
         LambdaData lambdaData = (LambdaData) unmarshaller.unmarshal(file);
         lambdaData.setLambdaFile(file);
         lambdaData.setLambdaRead(true);
         lambdaData.rectify();
         return lambdaData;
       } catch (Exception e) {
         logger.warning(" Exception reading LambdaData:\n " + e);
       }
     }
     LambdaData lambdaData = new LambdaData();
     lambdaData.setLambdaFile(file);
     lambdaData.rectify();
     return lambdaData;
   }
 
   /**
    * Marshall the lambda data to a file.
    */
   public void writeLambdaData() {
     writeLambdaData(this, lambdaFile);
   }
 
   public File getLambdaFile() {
     return lambdaFile;
   }
 
   public void setLambdaFile(@Nullable File lambdaFile) {
     this.lambdaFile = lambdaFile;
     if (lambdaFile != null) {
       lambdaFileName = FileUtils.relativePathTo(lambdaFile).toString();
     } else {
       lambdaFileName = null;
     }
   }
 
   public String getLambdaFileName() {
     return lambdaFileName;
   }
 
   public boolean wasLambdaRead() {
     return lambdaRead;
   }
 
   public void setLambdaRead(boolean lambdaRead) {
     this.lambdaRead = lambdaRead;
   }
 
   public void setHistogramIndex(int histogramIndex) {
     this.histogramIndex = histogramIndex;
   }
 
   public void setStepsTaken(int stepsTaken) {
     this.stepsTaken = stepsTaken;
   }
 }