// ******************************************************************************
   //
   // 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.pme;
  
  import edu.rit.pj.IntegerForLoop;
  import edu.rit.pj.IntegerSchedule;
  import edu.rit.pj.ParallelRegion;
  import edu.rit.pj.ParallelTeam;
  import ffx.crystal.Crystal;
  import ffx.crystal.SymOp;
  import ffx.potential.bonded.Atom;
  
  import java.util.List;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  /**
   * Parallel expansion of the asymmetric unit induced dipoles to symmetry mates by applying symmetry
   * operator rotation matrices.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class ExpandInducedDipolesRegion extends ParallelRegion {
  
    private static final Logger logger = Logger.getLogger(ExpandInducedDipolesRegion.class.getName());
    private final ExpandInducedDipoleLoop[] expandInducedDipoleLoop;
    /** Dimensions of [nsymm][nAtoms][3] */
    public double[][][] inducedDipole;
  
    public double[][][] inducedDipoleCR;
    /** An ordered array of atoms in the system. */
    private Atom[] atoms;
    /** Unit cell and spacegroup information. */
    private Crystal crystal;
  
    public ExpandInducedDipolesRegion(int maxThreads) {
      expandInducedDipoleLoop = new ExpandInducedDipoleLoop[maxThreads];
      for (int i = 0; i < maxThreads; i++) {
        expandInducedDipoleLoop[i] = new ExpandInducedDipoleLoop();
      }
    }
  
    /**
     * Execute the ExpandInducedDipolesRegion with the passed ParallelTeam.
     *
     * @param parallelTeam The ParallelTeam instance to execute with.
     */
    public void executeWith(ParallelTeam parallelTeam) {
      try {
        parallelTeam.execute(this);
      } catch (Exception e) {
        String message = " Exception expanding induced dipoles.\n";
        logger.log(Level.WARNING, message, e);
      }
    }
  
    public void init(
        Atom[] atoms, Crystal crystal, double[][][] inducedDipole, double[][][] inducedDipoleCR) {
      // Input
      this.atoms = atoms;
      this.crystal = crystal;
      // Output
      this.inducedDipole = inducedDipole;
     this.inducedDipoleCR = inducedDipoleCR;
   }
 
   @Override
   public void run() {
     try {
       int nAtoms = atoms.length;
       execute(0, nAtoms - 1, expandInducedDipoleLoop[getThreadIndex()]);
     } catch (Exception e) {
       String message =
           "Fatal exception expanding coordinates in thread: " + getThreadIndex() + "\n";
       logger.log(Level.SEVERE, message, e);
     }
   }
 
   private class ExpandInducedDipoleLoop extends IntegerForLoop {
 
     @Override
     public void run(int lb, int ub) {
       List<SymOp> symOps = crystal.spaceGroup.symOps;
       int nSymm = symOps.size();
       for (int s = 1; s < nSymm; s++) {
         SymOp symOp = symOps.get(s);
         for (int ii = lb; ii <= ub; ii++) {
           crystal.applySymRot(inducedDipole[0][ii], inducedDipole[s][ii], symOp);
           crystal.applySymRot(inducedDipoleCR[0][ii], inducedDipoleCR[s][ii], symOp);
         }
       }
     }
 
     @Override
     public IntegerSchedule schedule() {
       return IntegerSchedule.fixed();
     }
   }
 }