// ******************************************************************************
   //
   // 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.potential.nonbonded;
  
  import edu.rit.pj.IntegerForLoop;
  import edu.rit.pj.IntegerSchedule;
  import edu.rit.pj.ParallelRegion;
  import ffx.crystal.Crystal;
  import ffx.potential.bonded.Atom;
  
  import java.nio.DoubleBuffer;
  import java.util.logging.Level;
  
  import static ffx.potential.nonbonded.SpatialDensityRegion.logger;
  import static java.util.Arrays.fill;
  
  /**
   * The SliceLoop class is used to parallelize placing onto a 3D grid
   *
   * <p>1) Multipoles using B-splines or
   *
   * <p>2) Diffraction form factors.
   *
   * <p>Each "slice" of the grid (i.e. a fixed value of the z-coordinate) is operated on by only a
   * single thread to logically enforce atomic updates of grid magnitudes.
   *
   * @author Armin Avdic
   */
  public class SliceRegion extends ParallelRegion {
  
    public int buff = 3;
    public boolean[][] select;
    protected SliceLoop[] sliceLoop;
    protected double[][][] coordinates;
    int nAtoms;
    int nSymm;
    private int gX, gY, gZ;
    private DoubleBuffer gridBuffer;
    private GridInitLoop[] gridInitLoop;
    private double initValue = 0.0;
    private int gridSize;
    private double[] grid;
    private boolean rebuildList;
    private int[][] zAtListBuild;
  
    /**
     * Constructor for SliceRegion.
     *
     * @param gX a int.
     * @param gY a int.
     * @param gZ a int.
     * @param grid the grid array.
     * @param nSymm a int.
     * @param threadCount a int.
     * @param atoms an array of {@link ffx.potential.bonded.Atom} objects.
     * @param coordinates the atomic coordinate array.
     */
    public SliceRegion(int gX, int gY, int gZ, double[] grid, int nSymm,
        int threadCount, Atom[] atoms, double[][][] coordinates) {
      this.nAtoms = atoms.length;
      this.gX = gX;
      this.gY = gY;
      this.gZ = gZ;
      gridSize = gX * gY * gZ * 2;
     this.nSymm = nSymm;
     this.coordinates = coordinates;
     this.grid = grid;
     if (grid != null) {
       gridBuffer = DoubleBuffer.wrap(grid);
     }
     sliceLoop = new SliceLoop[threadCount];
     gridInitLoop = new GridInitLoop[threadCount];
     for (int i = 0; i < threadCount; i++) {
       gridInitLoop[i] = new GridInitLoop();
     }
     select = new boolean[nSymm][nAtoms];
     for (int i = 0; i < nSymm; i++) {
       fill(select[i], true);
     }
     zAtListBuild = new int[nSymm][nAtoms];
     rebuildList = true;
   }
 
   /** {@inheritDoc} */
   @Override
   public void finish() {
     if (rebuildList) {
       sliceLoop[0].saveZValues(zAtListBuild);
     }
     rebuildList = false;
   }
 
   /**
    * Getter for the field <code>grid</code>.
    *
    * @return return the grid array.
    */
   public double[] getGrid() {
     return grid;
   }
 
   /**
    * getNatoms.
    *
    * @return a int.
    */
   public int getNatoms() {
     return nAtoms;
   }
 
   /**
    * getNsymm.
    *
    * @return a int.
    */
   public int getNsymm() {
     return nSymm;
   }
 
   /** {@inheritDoc} */
   @Override
   public void run() throws Exception {
     int threadIndex = getThreadIndex();
     SliceLoop loop = sliceLoop[threadIndex];
     // This lets the same SpatialDensityLoops be used with different SpatialDensityRegions.
     loop.setNsymm(nSymm);
     loop.setRebuildList(rebuildList);
     try {
       execute(0, gridSize - 1, gridInitLoop[threadIndex]);
       execute(0, gZ - 1, loop);
     } catch (Exception e) {
       String message = " Exception in SliceRegion.";
       logger.log(Level.SEVERE, message, e);
     }
   }
 
   /**
    * Select atoms that should be included. The default is to include all atoms, which is set up in
    * the constructor. This function should be over-ridden by subclasses that want finer control.
    */
   public void selectAtoms() {
     for (int i = 0; i < nSymm; i++) {
       fill(select[i], true);
     }
   }
 
   /**
    * Setter for the field <code>atoms</code>.
    *
    * @param atoms an array of {@link ffx.potential.bonded.Atom} objects.
    */
   public void setAtoms(Atom[] atoms) {
     nAtoms = atoms.length;
     select = new boolean[nSymm][nAtoms];
     zAtListBuild = new int[nSymm][nAtoms];
     for (int i = 0; i < nSymm; i++) {
       fill(select[i], true);
     }
     rebuildList = true;
   }
 
   /**
    * Setter for the field <code>crystal</code>.
    *
    * @param crystal a {@link ffx.crystal.Crystal} object.
    * @param gX a int.
    * @param gY a int.
    * @param gZ a int.
    */
   public final void setCrystal(Crystal crystal, int gX, int gY, int gZ) {
     // this.crystal = crystal.getUnitCell();
     this.gX = gX;
     this.gY = gY;
     this.gZ = gZ;
     gridSize = gX * gY * gZ * 2;
   }
 
   /**
    * setDensityLoop.
    *
    * @param loops an array of {@link ffx.potential.nonbonded.SliceLoop} objects.
    */
   public void setDensityLoop(SliceLoop[] loops) {
     sliceLoop = loops;
   }
 
   /**
    * Setter for the field <code>initValue</code>.
    *
    * @param initValue a double.
    */
   public void setInitValue(double initValue) {
     this.initValue = initValue;
   }
 
   /** {@inheritDoc} */
   @Override
   public void start() {
     selectAtoms();
     rebuildList = (rebuildList || sliceLoop[0].checkList(zAtListBuild, buff));
   }
 
   /**
    * Setter for the field <code>gridBuffer</code>.
    *
    * @param grid a {@link java.nio.DoubleBuffer} object.
    */
   void setGridBuffer(DoubleBuffer grid) {
     gridBuffer = grid;
   }
 
   private class GridInitLoop extends IntegerForLoop {
 
     private final IntegerSchedule schedule = IntegerSchedule.fixed();
 
     @Override
     public void run(int lb, int ub) {
       if (gridBuffer != null) {
         // if (grid != null) {
         for (int i = lb; i <= ub; i++) {
           // grid[i] = initValue;
           gridBuffer.put(i, initValue);
         }
       }
     }
 
     @Override
     public IntegerSchedule schedule() {
       return schedule;
     }
   }
 }