// ******************************************************************************
   //
   // 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
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  // exception statement from your version.
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  // ******************************************************************************
  package ffx.potential.bonded;
  
  import ffx.numerics.atomic.AtomicDoubleArray3D;
  import ffx.potential.parameters.ForceField;
  import ffx.potential.parameters.UreyBradleyType;
  
  import java.io.Serial;
  import java.util.logging.Logger;
  
  /**
   * The UreyBradley class.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class UreyBradley extends BondedTerm {
  
    @Serial
    private static final long serialVersionUID = 1L;
  
    private static final Logger logger = Logger.getLogger(UreyBradley.class.getName());
  
    /**
     * Force field parameters to compute the Stretch-Bend energy.
     */
    public final UreyBradleyType ureyBradleyType;
    /**
     * The Angle this UreyBradley term is based on.
     */
    protected final Angle angle;
    /**
     * Scale factor to apply to Urey-Bradley term.
     */
    private double rigidScale = 1.0;
  
    /**
     * Constructor for the UreyBradley class.
     *
     * @param a               a {@link ffx.potential.bonded.Angle} object.
     * @param ureyBradleyType The Urey-Bradley type to apply.
     */
    public UreyBradley(Angle a, UreyBradleyType ureyBradleyType) {
      super();
      angle = a;
      bonds = a.bonds;
      atoms = a.atoms;
      this.ureyBradleyType = ureyBradleyType;
      setID_Key(false);
    }
  
    /**
     * Attempt to create a new UreyBradley for the specified Angle.
     *
     * @param angle      the Angle to create the UreyBradley from.
     * @param forceField the ForceField parameters to apply.
     * @return a new UreyBradley, or null.
     */
    public static UreyBradley ureyBradlyFactory(Angle angle, ForceField forceField) {
      if (angle == null) {
        return null;
      }
      UreyBradleyType ureyBradleyType = forceField.getUreyBradleyType(angle.angleType.getKey());
     if (ureyBradleyType == null) {
       return null;
     }
     return new UreyBradley(angle, ureyBradleyType);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public int compareTo(BondedTerm ub) {
     if (!ub.getClass().isInstance(this)) {
       return super.compareTo(ub);
     }
     return angle.compareTo(((UreyBradley) ub).angle);
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Evaluate the Urey-Bradley energy.
    */
   @Override
   public double energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad) {
     value = 0.0;
     energy = 0.0;
     // Only compute this term if at least one atom is being used.
     if (!getUse()) {
       return energy;
     }
     var atomA = atoms[0];
     var atomC = atoms[2];
     var va = atomA.getXYZ();
     var vc = atomC.getXYZ();
     var vac = va.sub(vc);
     value = vac.length();
     var dv = value - ureyBradleyType.distance;
     var dv2 = dv * dv;
     energy = ureyBradleyType.ureyUnit * rigidScale * ureyBradleyType.forceConstant * dv2
         * (1.0 + ureyBradleyType.cubic * dv + ureyBradleyType.quartic * dv2);
     if (gradient) {
       var deddt = 2.0 * ureyBradleyType.ureyUnit * rigidScale * ureyBradleyType.forceConstant * dv
           * (1.0 + 1.5 * ureyBradleyType.cubic * dv + 2.0 * ureyBradleyType.quartic * dv2);
       var de = 0.0;
       if (value > 0.0) {
         de = deddt / value;
       }
       var ia = atomA.getIndex() - 1;
       var ic = atomC.getIndex() - 1;
       grad.add(threadID, ia, vac.scaleI(de));
       grad.sub(threadID, ic, vac);
     }
     return energy;
   }
 
   /**
    * log
    */
   public void log() {
     logger.info(
         String.format(" %s %6d-%s %6d-%s %6.4f  %6.4f  %10.4f", "Urey-Bradley", atoms[0].getIndex(),
             atoms[0].getAtomType().name, atoms[2].getIndex(), atoms[2].getAtomType().name,
             ureyBradleyType.distance, value, energy));
   }
 
   /**
    * Setter for the field <code>rigidScale</code>.
    *
    * @param rigidScale a double.
    */
   public void setRigidScale(double rigidScale) {
     this.rigidScale = rigidScale;
   }
 }