// ******************************************************************************
   //
   // 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.terms;
  
  import edu.rit.pj.reduction.SharedDouble;
  import ffx.potential.bonded.BondedTerm;
  
  import java.util.logging.Logger;
  
  import static org.apache.commons.math3.util.FastMath.sqrt;
  
  /**
   * Base class for potential energy terms used by ForceFieldEnergy.
   * <p>
   * This abstract class holds minimal, common metadata shared by energy terms:
   * a human-readable name and an integer force-group identifier. Specific energy
   * terms (bonded, nonbonded, restraints, etc.) should extend this class.
   */
  public abstract class EnergyTerm {
  
    private static final Logger logger = Logger.getLogger(EnergyTerm.class.getName());
  
    /**
     * Optional name for this energy term (for reporting/logging).
     */
    protected String name;
  
    /**
     * Integer force group this term belongs to. Defaults to 0.
     */
    protected int forceGroup = 0;
  
    /**
     * Total potential energy for this term.
     */
    protected SharedDouble energy = new SharedDouble();
  
    /**
     * Shared double for RMSD calculations.
     */
    private final SharedDouble sharedRMSD = new SharedDouble();
  
    /**
     * The time taken to compute the energy for this term in nanoseconds.
     */
    private long computeTime = 0L;
  
    /**
     * Create an unnamed EnergyTerm with default force group 0.
     */
    protected EnergyTerm() {
    }
  
    /**
     * Create a named EnergyTerm with default force group 0.
     *
     * @param name Name for this energy term.
     */
    protected EnergyTerm(String name) {
      this.name = name;
    }
  
    /**
     * Create a named EnergyTerm with a specified force group.
    *
    * @param name       Name for this energy term.
    * @param forceGroup Integer force group identifier.
    */
   protected EnergyTerm(String name, int forceGroup) {
     this.name = name;
     this.forceGroup = forceGroup;
   }
 
   /**
    * Get the number of BondedTerms in this term.
    *
    * @return The number of BondedTerms.
    */
   abstract public int getNumberOfTerms();
 
   /**
    * Get an array of BondedTerms in this term.
    *
    * @return Array of BondedTerms.
    */
   abstract public BondedTerm[] getBondedTermsArray();
 
   /**
    * Log the details of this energy term.
    */
   abstract public void log();
 
   /**
    * Get a string representation of this energy term.
    *
    * @return A string representation of the energy term.
    */
   abstract public String toString();
 
   /**
    * Get a PDB-style REMARK representation of this energy term.
    * @return A PDB REMARK string for this energy term.
    */
   abstract public String toPDBString();
 
   /**
    * Get the current force group identifier.
    *
    * @return force group as an int
    */
   public int getForceGroup() {
     return forceGroup;
   }
 
   /**
    * Set the force group identifier.
    *
    * @param forceGroup integer force group
    */
   public void setForceGroup(int forceGroup) {
     this.forceGroup = forceGroup;
   }
 
   /**
    * Get the name of this energy term.
    *
    * @return name (may be null)
    */
   public String getName() {
     return name;
   }
 
   /**
    * Set the name of this energy term.
    *
    * @param name A human-readable name
    */
   public void setName(String name) {
     this.name = name;
   }
 
   /**
    * Get the total potential energy of this term.
    *
    * @return Energy value as a double.
    */
   public double getEnergy() {
     return energy.get();
   }
 
   /**
    * Set the total potential energy of this term.
    *
    * @param e Energy value to set.
    */
   protected void setEnergy(double e) {
     energy.set(e);
   }
 
   /**
    * Add energy to the total energy for this term and return the new total.
    *
    * @param e Energy value to add to the total.
    * @return The new total energy after adding the provided energy.
    */
   protected double addAndGetEnergy(double e) {
     return energy.addAndGet(e);
   }
 
   /**
    * Set the RMSD accumulator value for this term.
    *
    * @param rmsd RMSD value to set for this term.
    */
   protected void setRMSD(double rmsd) {
     sharedRMSD.set(rmsd);
   }
 
   /**
    * Get the RMSD for this term.
    */
   public double getRMSD() {
     return sqrt(sharedRMSD.get() / getNumberOfTerms());
   }
 
   /**
    * Add RMSD to the shared RMSD and return the new total.
    *
    * @param rmsd RMSD value to add to the shared RMSD.
    * @return The new total RMSD after adding the provided value.
    */
   protected double addAndGetRMSD(double rmsd) {
     return sharedRMSD.addAndGet(rmsd);
   }
 
   /**
    * Set the starting time for the energy computation.
    */
   protected void startTime() {
     computeTime = -System.nanoTime();
   }
 
   /**
    * Stop the timer for the energy computation.
    */
   public void stopTime() {
     computeTime += System.nanoTime();
   }
 
   /**
    * Get the time taken to compute the energy for this term in seconds.
    *
    * @return The time in seconds.
    */
   public double getTime() {
     return computeTime * 1.0e-9;
   }
 
 
 }