// ******************************************************************************
   //
   // 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.algorithms;
  
  import ffx.algorithms.dynamics.MolecularDynamics;
  import ffx.algorithms.dynamics.integrators.IntegratorEnum;
  import ffx.algorithms.dynamics.thermostats.ThermostatEnum;
  import ffx.algorithms.optimize.Minimize;
  import ffx.numerics.Potential;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.utils.PotentialsUtils;
  
  import java.io.File;
  import java.util.logging.Logger;
  
  /**
   * AlgorithmUtils, on top of the core functionality of PotentialsUtils, implements additional
   * functionality such as molecular dynamics and L-BFGS local optimization. This implementation does
   * not do anything on top of what is specified by the interface, and is used primarily by tests. It
   * is also potentially useful for third parties who would like to use FFX without its graphical user
   * interface.
   *
   * @author Jacob M. Litman
   * @author Michael J. Schnieders
   */
  public class AlgorithmUtils extends PotentialsUtils implements AlgorithmFunctions {
  
    private static final Logger logger = Logger.getLogger(AlgorithmUtils.class.getName());
    private final long initTime;
    private long interTime;
  
    /** Constructor for AlgorithmUtils. */
    public AlgorithmUtils() {
      initTime = System.nanoTime();
      interTime = initTime;
    }
  
    /**
     * {@inheritDoc}
     *
     * <p>Performs molecular dynamics on a MolecularAssembly.
     */
    @Override
    public void md(MolecularAssembly assembly, int nStep, double timeStep, double printInterval,
        double saveInterval, double temperature, boolean initVelocities, File dyn) {
      if (assembly == null) {
        logger.info(" No active system to minimize.");
      } else {
        MolecularDynamics molecularDynamics = new MolecularDynamics(assembly,
            assembly.getPotentialEnergy(), null, ThermostatEnum.BUSSI, IntegratorEnum.BEEMAN);
        molecularDynamics.dynamic(nStep, timeStep, printInterval, saveInterval, temperature,
            initVelocities, dyn);
      }
    }
  
    /**
     * {@inheritDoc}
     *
     * <p>Minimizes a MolecularAssembly using AMOEBA potential energy.
     */
    @Override
    public Potential minimize(MolecularAssembly assembly, double eps) {
      if (assembly == null) {
        logger.info(" No active system to minimize.");
       return null;
     } else {
       Minimize minimize = new Minimize(assembly, null);
       return minimize.minimize(eps);
     }
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Logs time since this interface was created and the last time this method was called. May be
    * more elegant to replace this by using protected variables and simply inheriting the time()
    * function.
    */
   @Override
   public double time() {
     long currTime = System.nanoTime();
     logger.info(
         String.format(" Time since interface established: %f", (currTime - initTime) * 1.0E-9));
     double elapsed = (currTime - interTime) * 1.0E-9;
     interTime = currTime;
     logger.info(String.format(" Time since last timer call: %f", elapsed));
     return elapsed;
   }
 }