// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2025.
   //
   // 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.numerics.atomic;
  
  import edu.rit.pj.IntegerForLoop;
  import edu.rit.pj.ParallelRegion;
  import edu.rit.pj.ParallelTeam;
  import edu.rit.pj.reduction.SharedDoubleArray;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  /**
   * PJDoubleArray implements the AtomicDoubleArray interface using the Parallel Java class
   * SharedDoubleArray.
   *
   * <p>SharedDoubleArray is multiple thread safe and uses lock-free atomic compare-and-set.
   *
   * <p>Note: Class SharedDoubleArray is implemented using class
   * java.util.concurrent.atomic.AtomicLongArray. Each double array element is stored as a long whose
   * bit pattern is the same as the double value.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class PJDoubleArray implements AtomicDoubleArray {
  
    private static final Logger logger = Logger.getLogger(PJDoubleArray.class.getName());
  
    private SharedDoubleArray array;
    private int arraySize;
  
    /**
     * Constructor: Initialize the size and array.
     *
     * @param arraySize the desired size of the array.
     */
    public PJDoubleArray(int arraySize) {
      this.arraySize = arraySize;
      this.array = new SharedDoubleArray(arraySize);
    }
  
    /**
     * {@inheritDoc}
     */
    @Override
    public void add(final int threadID, final int index, final double value) {
      array.getAndAdd(index, value);
    }
  
    /**
     * {@inheritDoc}
     */
    @Override
    public void alloc(final int newSize) {
      this.arraySize = newSize;
      if (array.length() < newSize) {
        array = new SharedDoubleArray(newSize);
      }
    }
  
    /**
     * {@inheritDoc}
     */
    @Override
   public double get(final int index) {
     return array.get(index);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void reduce(final int lowerBound, final int upperBound) {
     // Intentionally left empty: handled atomically by SharedDoubleArray.
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void reduce(final ParallelTeam parallelTeam, final int lowerBound, final int upperBound) {
     // Intentionally left empty: handled atomically by SharedDoubleArray.
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void reset(final int threadID, final int lowerBound, final int upperBound) {
     resetSerially(lowerBound, upperBound);
   }
 
   /**
    * Reset elements serially to 0.0 in the given range.
    *
    * @param lowerBound inclusive start index.
    * @param upperBound inclusive end index.
    */
   private void resetSerially(final int lowerBound, final int upperBound) {
     for (int i = lowerBound; i <= upperBound; i++) {
       array.set(i, 0.0);
     }
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void reset(final ParallelTeam parallelTeam, final int lowerBound, final int upperBound) {
     try {
       parallelTeam.execute(
           new ParallelRegion() {
             @Override
             public void run() throws Exception {
               execute(
                   lowerBound,
                   upperBound,
                   new IntegerForLoop() {
                     @Override
                     public void run(final int first, final int last) {
                       resetSerially(first, last);
                     }
                   });
             }
           });
     } catch (Exception e) {
       logger.log(Level.WARNING, "Exception resetting a PJDoubleArray", e);
     }
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void scale(final int threadID, final int index, final double value) {
     final double current = array.get(index);
     array.getAndSet(index, current * value);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void set(final int threadID, final int index, final double value) {
     array.getAndSet(index, value);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public int size() {
     return arraySize;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void sub(final int threadID, final int index, final double value) {
     array.getAndAdd(index, -value);
   }
 }