// ******************************************************************************
   //
   // 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.
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  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
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  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
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  // combined work based on this library. Thus, the terms and conditions of the
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  // ******************************************************************************
  package ffx.potential.openmm;
  
  import ffx.openmm.Force;
  import ffx.openmm.HarmonicBondForce;
  import ffx.potential.ForceFieldEnergy;
  import ffx.potential.bonded.UreyBradley;
  import ffx.potential.parameters.UreyBradleyType;
  import ffx.potential.terms.UreyBradleyPotentialEnergy;
  
  import java.util.logging.Logger;
  
  import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_KJPerKcal;
  import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_NmPerAngstrom;
  import static java.lang.String.format;
  
  /**
   * Urey-Bradley Force.
   */
  public class UreyBradleyForce extends HarmonicBondForce {
  
    private static final Logger logger = Logger.getLogger(UreyBradleyForce.class.getName());
  
    /**
     * Urey-Bradly Force constructor.
     *
     * @param ureyBradleyPotentialEnergy The UreyBradleyPotentialEnergy instance.
     */
    public UreyBradleyForce(UreyBradleyPotentialEnergy ureyBradleyPotentialEnergy) {
      UreyBradley[] ureyBradleys = ureyBradleyPotentialEnergy.getUreyBradleyArray();
      double kParameterConversion = OpenMM_KJPerKcal / (OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom);
  
      for (UreyBradley ureyBradley : ureyBradleys) {
        int i1 = ureyBradley.getAtom(0).getArrayIndex();
        int i2 = ureyBradley.getAtom(2).getArrayIndex();
        UreyBradleyType ureyBradleyType = ureyBradley.ureyBradleyType;
        double length = ureyBradleyType.distance * OpenMM_NmPerAngstrom;
        // The implementation of UreyBradley in FFX & Tinker: k x^2
        // The implementation of Harmonic Bond Force in OpenMM:  k x^2 / 2
        double k = 2.0 * ureyBradleyType.forceConstant * ureyBradleyType.ureyUnit * kParameterConversion;
        addBond(i1, i2, length, k);
      }
  
      int forceGroup = ureyBradleyPotentialEnergy.getForceGroup();
      setForceGroup(forceGroup);
      logger.info(format("  Urey-Bradleys:                     %10d", ureyBradleys.length));
      logger.fine(format("   Force Group:                      %10d", forceGroup));
    }
  
    /**
     * Urey-Bradly Force constructor.
     *
     * @param topology                 The topology index for the OpenMM System.
     * @param openMMDualTopologyEnergy The OpenMMDualTopologyEnergy instance.
     */
    public UreyBradleyForce(UreyBradleyPotentialEnergy ureyBradleyPotentialEnergy,
                            int topology, OpenMMDualTopologyEnergy openMMDualTopologyEnergy) {
      UreyBradley[] ureyBradleys = ureyBradleyPotentialEnergy.getUreyBradleyArray();
      double scale = openMMDualTopologyEnergy.getTopologyScale(topology);
      double kParameterConversion = OpenMM_KJPerKcal / (OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom);
  
      for (UreyBradley ureyBradley : ureyBradleys) {
        int i1 = ureyBradley.getAtom(0).getArrayIndex();
       int i2 = ureyBradley.getAtom(2).getArrayIndex();
       UreyBradleyType ureyBradleyType = ureyBradley.ureyBradleyType;
       double length = ureyBradleyType.distance * OpenMM_NmPerAngstrom;
       // The implementation of UreyBradley in FFX & Tinker: k x^2
       // The implementation of Harmonic Bond Force in OpenMM:  k x^2 / 2
       double k = 2.0 * ureyBradleyType.forceConstant * ureyBradleyType.ureyUnit * kParameterConversion;
       // Don't apply lambda scale to alchemical Urey-Bradley
       if (!ureyBradley.applyLambda()) {
         k = k * scale;
       }
       i1 = openMMDualTopologyEnergy.mapToDualTopologyIndex(topology, i1);
       i2 = openMMDualTopologyEnergy.mapToDualTopologyIndex(topology, i2);
       addBond(i1, i2, length, k);
     }
 
     int forceGroup = ureyBradleyPotentialEnergy.getForceGroup();
     setForceGroup(forceGroup);
     logger.info(format("  Urey-Bradleys:                     %10d", ureyBradleys.length));
     logger.fine(format("   Force Group:                      %10d", forceGroup));
   }
 
   /**
    * Convenience method to construct an OpenMM Urey-Bradley Force.
    *
    * @param openMMEnergy The OpenMM Energy instance that contains the angles.
    * @return An OpenMM Urey-Bradley Force, or null if there are no Urey-Bradley.
    */
   public static Force constructForce(OpenMMEnergy openMMEnergy) {
     UreyBradleyPotentialEnergy ureyBradleyPotentialEnergy = openMMEnergy.getUreyBradleyPotentialEnergy();
     if (ureyBradleyPotentialEnergy == null) {
       return null;
     }
     return new UreyBradleyForce(ureyBradleyPotentialEnergy);
   }
 
   /**
    * Convenience method to construct an OpenMM Urey-Bradley Force.
    *
    * @param topology                 The topology index for the OpenMM System.
    * @param openMMDualTopologyEnergy The OpenMMDualTopologyEnergy instance.
    */
   public static Force constructForce(int topology, OpenMMDualTopologyEnergy openMMDualTopologyEnergy) {
     ForceFieldEnergy forceFieldEnergy = openMMDualTopologyEnergy.getForceFieldEnergy(topology);
     UreyBradleyPotentialEnergy ureyBradleyPotentialEnergy = forceFieldEnergy.getUreyBradleyPotentialEnergy();
     if (ureyBradleyPotentialEnergy == null) {
       return null;
     }
     return new UreyBradleyForce(ureyBradleyPotentialEnergy, topology, openMMDualTopologyEnergy);
   }
 
   /**
    * Update the Urey-Bradley parameters in the OpenMM Context.
    *
    * @param openMMEnergy The OpenMM Energy instance that contains the Urey-Bradley terms.
    */
   public void updateForce(OpenMMEnergy openMMEnergy) {
     UreyBradleyPotentialEnergy ureyBradleyPotentialEnergy = openMMEnergy.getUreyBradleyPotentialEnergy();
     if (ureyBradleyPotentialEnergy == null) {
       return;
     }
     UreyBradley[] ureyBradleys = ureyBradleyPotentialEnergy.getUreyBradleyArray();
     double kParameterConversion = OpenMM_KJPerKcal / (OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom);
 
     int index = 0;
     for (UreyBradley ureyBradley : ureyBradleys) {
       int i1 = ureyBradley.getAtom(0).getArrayIndex();
       int i2 = ureyBradley.getAtom(2).getArrayIndex();
       UreyBradleyType ureyBradleyType = ureyBradley.ureyBradleyType;
       double length = ureyBradleyType.distance * OpenMM_NmPerAngstrom;
       // The implementation of UreyBradley in FFX & Tinker: k x^2
       // The implementation of Harmonic Bond Force in OpenMM:  k x^2 / 2
       double k = 2.0 * ureyBradleyType.forceConstant * ureyBradleyType.ureyUnit * kParameterConversion;
       setBondParameters(index++, i1, i2, length, k);
     }
 
     updateParametersInContext(openMMEnergy.getContext());
   }
 
   /**
    * Update the Urey-Bradley parameters in the OpenMM Context.
    *
    * @param topology                 The topology index for the OpenMM System.
    * @param openMMDualTopologyEnergy The OpenMMDualTopologyEnergy instance.
    */
   public void updateForce(int topology, OpenMMDualTopologyEnergy openMMDualTopologyEnergy) {
     ForceFieldEnergy forceFieldEnergy = openMMDualTopologyEnergy.getForceFieldEnergy(topology);
     UreyBradleyPotentialEnergy forceFieldEnergyUreyBradley =
         forceFieldEnergy.getUreyBradleyPotentialEnergy();
     if (forceFieldEnergyUreyBradley == null) {
       return;
     }
     UreyBradley[] ureyBradleys = forceFieldEnergyUreyBradley.getUreyBradleyArray();
     double scale = openMMDualTopologyEnergy.getTopologyScale(topology);
     double kParameterConversion = OpenMM_KJPerKcal / (OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom);
 
     int index = 0;
     for (UreyBradley ureyBradley : ureyBradleys) {
       int i1 = ureyBradley.getAtom(0).getArrayIndex();
       int i2 = ureyBradley.getAtom(2).getArrayIndex();
       UreyBradleyType ureyBradleyType = ureyBradley.ureyBradleyType;
       double length = ureyBradleyType.distance * OpenMM_NmPerAngstrom;
       // The implementation of UreyBradley in FFX & Tinker: k x^2
       // The implementation of Harmonic Bond Force in OpenMM:  k x^2 / 2
       double k = 2.0 * ureyBradleyType.forceConstant * ureyBradleyType.ureyUnit * kParameterConversion;
       // Don't apply lambda scale to alchemical Urey-Bradley
       if (!ureyBradley.applyLambda()) {
         k = k * scale;
       }
       i1 = openMMDualTopologyEnergy.mapToDualTopologyIndex(topology, i1);
       i2 = openMMDualTopologyEnergy.mapToDualTopologyIndex(topology, i2);
       setBondParameters(index++, i1, i2, length, k);
     }
 
     updateParametersInContext(openMMDualTopologyEnergy.getContext());
   }
 
 }