// ******************************************************************************
   //
   // 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.xray.solvent;
  
  import edu.rit.pj.ParallelTeam;
  import ffx.crystal.Crystal;
  import ffx.potential.bonded.Atom;
  import ffx.potential.nonbonded.RowRegion;
  
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  import static java.util.Arrays.fill;
  
  /**
   * This class implements a spatial decomposition based on partitioning a grid into rows. The
   * over-ridden "selectAtoms" method selects atoms that are not in the asymmetric unit, but are
   * within the supplied cutoff radius.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class BulkSolventRowRegion extends RowRegion {
  
    /** Constant <code>logger</code> */
    protected static final Logger logger = Logger.getLogger(BulkSolventRowRegion.class.getName());
  
    private final BulkSolventList bulkSolventList;
    private final int gZ;
    private final int gY;
  
    /**
     * Constructor for BulkSolventDensityRegion.
     *
     * @param gX a int.
     * @param gY a int.
     * @param gZ a int.
     * @param grid an array of double.
     * @param nSymm a int.
     * @param threadCount a int.
     * @param crystal a {@link ffx.crystal.Crystal} object.
     * @param atoms an array of {@link ffx.potential.bonded.Atom} objects.
     * @param coordinates an array of double.
     * @param cutoff a double.
     * @param parallelTeam a {@link edu.rit.pj.ParallelTeam} object.
     */
    public BulkSolventRowRegion(int gX, int gY, int gZ, double[] grid, int nSymm,
        int threadCount, Crystal crystal, Atom[] atoms, double[][][] coordinates, double cutoff,
        ParallelTeam parallelTeam) {
      super(gX, gY, gZ, grid, nSymm, threadCount, atoms, coordinates);
      this.gZ = gZ;
      this.gY = gY;
      // Asymmetric unit atoms never selected by this class.
      fill(select[0], false);
      bulkSolventList = new BulkSolventList(crystal, atoms, cutoff, parallelTeam);
    }
  
    /** {@inheritDoc} */
    @Override
    public void run() {
      try {
        execute(0, (gZ * gY) - 1, rowLoop[getThreadIndex()]);
      } catch (Exception e) {
        String message = " Exception in BulkSolventRowRegion.";
       logger.log(Level.SEVERE, message, e);
     }
   }
 
   /** {@inheritDoc} */
   @Override
   public void selectAtoms() {
     bulkSolventList.buildList(coordinates, select, false);
   }
 }