// ******************************************************************************
   //
   // 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 java.util.Arrays;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  /**
   * The MultiDoubleArray avoids the need for Atomic variables, but at the cost of storing a full size
   * double array for each thread.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class MultiDoubleArray implements AtomicDoubleArray {
  
    private static final Logger logger = Logger.getLogger(MultiDoubleArray.class.getName());
  
    private final int threadCount;
  
    /**
     * Storage of the array.
     * <p>
     * First dimension is the thread. Second dimension is the value.
     */
    private final double[][] array;
  
    private int size;
  
    /**
     * Constructor for MultiDoubleArray.
     *
     * @param nThreads the number of threads.
     * @param size the size of the array.
     */
    public MultiDoubleArray(int nThreads, int size) {
      this.size = size;
      array = new double[nThreads][size];
      threadCount = nThreads;
    }
  
    /** {@inheritDoc} */
    @Override
    public void add(int threadID, int index, double value) {
      array[threadID][index] += value;
    }
  
    /** {@inheritDoc} */
    @Override
    public void alloc(int size) {
      this.size = size;
      for (int i = 0; i < threadCount; i++) {
        if (array[i].length < size) {
          array[i] = new double[size];
        }
      }
    }
  
    /**
     * {@inheritDoc}
    */
   @Override
   public double get(int index) {
     return array[0][index];
   }
 
   /**
    * {@inheritDoc}
    * <p>
    * Reduce the contributions from each thread into array[0];
    */
   @Override
   public void reduce(int lb, int ub) {
     double[] gx = array[0];
     for (int t = 1; t < threadCount; t++) {
       double[] gxt = array[t];
       for (int i = lb; i <= ub; i++) {
         gx[i] += gxt[i];
       }
     }
   }
 
   /**
    * {@inheritDoc}
    * <p>
    * Reduce the contributions from each thread into array[0];
    */
   @Override
   public void reduce(ParallelTeam parallelTeam, int lb, int ub) {
     try {
       parallelTeam.execute(
           new ParallelRegion() {
             @Override
             public void run() throws Exception {
               execute(
                   lb,
                   ub,
                   new IntegerForLoop() {
                     @Override
                     public void run(int first, int last) {
                       reduce(first, last);
                     }
                   });
             }
           });
     } catch (Exception e) {
       logger.log(Level.WARNING, " Exception reducing an MultiDoubleArray", e);
     }
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void reset(int threadID, int lb, int ub) {
     // Note that fill is appears slightly faster than arraycopy for 10,000 to 100,000 elements.
     Arrays.fill(array[threadID], 0.0);
     // System.arraycopy(zeros, 0, array[threadID], 0, size);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void reset(ParallelTeam parallelTeam, int lb, int ub) {
     try {
       parallelTeam.execute(
           new ParallelRegion() {
             @Override
             public void run() throws Exception {
               execute(
                   0,
                   threadCount - 1,
                   new IntegerForLoop() {
                     @Override
                     public void run(int first, int last) {
                       for (int i = first; i <= last; i++) {
                         reset(i, lb, ub);
                       }
                     }
                   });
             }
           });
     } catch (Exception e) {
       logger.log(Level.WARNING, " Exception resetting an MultiDoubleArray", e);
     }
   }
 
   /** {@inheritDoc} */
   @Override
   public void scale(int threadID, int index, double value) {
     array[threadID][index] *= value;
   }
 
   /** {@inheritDoc} */
   @Override
   public void set(int threadID, int index, double value) {
     array[threadID][index] = value;
   }
 
   /** {@inheritDoc} */
   @Override
   public int size() {
     return size;
   }
 
   /** {@inheritDoc} */
   @Override
   public void sub(int threadID, int index, double value) {
     array[threadID][index] -= value;
   }
 }