//******************************************************************************
   //
   // 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.commands;
  
  import ffx.algorithms.cli.AlgorithmsCommand;
  import ffx.algorithms.cli.AnnealOptions;
  import ffx.algorithms.cli.DynamicsOptions;
  import ffx.algorithms.optimize.anneal.SimulatedAnnealing;
  import ffx.numerics.Potential;
  import ffx.potential.cli.AtomSelectionOptions;
  import ffx.potential.cli.WriteoutOptions;
  import ffx.utilities.FFXBinding;
  import org.apache.commons.io.FilenameUtils;
  import picocli.CommandLine.Command;
  import picocli.CommandLine.Mixin;
  import picocli.CommandLine.Parameters;
  
  import java.io.File;
  import java.util.Collections;
  import java.util.List;
  
  import static java.lang.String.format;
  
  /**
   * The Anneal script.
   * <br>
   * Usage:
   * <br>
   * ffxc Anneal [options] &lt;filename&gt;
   */
  @Command(description = " Run simulated annealing on a system.", name = "Anneal")
  public class Anneal extends AlgorithmsCommand {
  
    @Mixin
    private AtomSelectionOptions atomSelectionOptions;
  
    @Mixin
    private DynamicsOptions dynamics;
  
    @Mixin
    private AnnealOptions anneal;
  
    @Mixin
    private WriteoutOptions writeOut;
  
    /**
     * An XYZ or PDB input file.
     */
    @Parameters(arity = "1", paramLabel = "file",
        description = "XYZ or PDB input file.")
    private String filename;
  
    private SimulatedAnnealing simulatedAnnealing = null;
  
    private Potential potential;
  
    /**
     * Anneal Constructor.
     */
    public Anneal() {
      super();
    }
  
    /**
    * Anneal Constructor.
    *
    * @param binding The Binding to use.
    */
   public Anneal(FFXBinding binding) {
     super(binding);
   }
 
   /**
    * Anneal constructor that sets the command line arguments.
    *
    * @param args Command line arguments.
    */
   public Anneal(String[] args) {
     super(args);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public Anneal run() {
 
     // Init the context and bind variables.
     if (!init()) {
       return this;
     }
 
     // Init DynamicsOptions (e.g. the thermostat and barostat flags).
     dynamics.init();
 
     // Load the MolecularAssembly.
     activeAssembly = getActiveAssembly(filename);
     if (activeAssembly == null) {
       logger.info(helpString());
       return this;
     }
 
     // Set the filename.
     filename = activeAssembly.getFile().getAbsolutePath();
 
     // Set active atoms.
     atomSelectionOptions.setActiveAtoms(activeAssembly);
 
     logger.info("\n Running simulated annealing on " + filename + "\n");
 
     // Define the path to the restart File.
     File dyn = new File(FilenameUtils.removeExtension(filename) + ".dyn");
     if (!dyn.exists()) {
       dyn = null;
     }
 
     potential = activeAssembly.getPotentialEnergy();
 
     simulatedAnnealing = anneal.createAnnealer(dynamics, activeAssembly,
         activeAssembly.getPotentialEnergy(), algorithmListener, dyn);
 
     simulatedAnnealing.setPrintInterval(dynamics.getReport());
     simulatedAnnealing.setSaveFrequency(dynamics.getWrite());
     simulatedAnnealing.setRestartFrequency(dynamics.getCheckpoint());
     simulatedAnnealing.setTrajectorySteps(dynamics.getTrajSteps());
 
     simulatedAnnealing.anneal();
 
     if (baseDir == null || !baseDir.exists() || !baseDir.isDirectory() || !baseDir.canWrite()) {
       baseDir = new File(FilenameUtils.getFullPath(filename));
     }
 
     String dirName = baseDir.toString() + File.separator;
     String fileName = FilenameUtils.getName(filename);
     fileName = FilenameUtils.removeExtension(fileName);
 
     writeOut.saveFile(format("%s%s", dirName, fileName), algorithmFunctions, activeAssembly);
 
     return this;
   }
 
   /**
    * Get the SimulatedAnnealing object.
    *
    * @return The SimulatedAnnealing instance.
    */
   public SimulatedAnnealing getAnnealing() {
     return simulatedAnnealing;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public List<Potential> getPotentials() {
     List<Potential> potentials;
     if (potential == null) {
       potentials = Collections.emptyList();
     } else {
       potentials = Collections.singletonList(potential);
     }
     return potentials;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public boolean destroyPotentials() {
     return getPotentials().stream().allMatch(Potential::destroy);
   }
 }