//******************************************************************************
   //
   // 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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  // library, you may extend this exception to your version of the library, but
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  // exception statement from your version.
  //
  //******************************************************************************
  package ffx.realspace.commands;
  
  import ffx.algorithms.cli.AlgorithmsCommand;
  import ffx.algorithms.cli.DynamicsOptions;
  import ffx.algorithms.dynamics.MolecularDynamics;
  import ffx.numerics.Potential;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.cli.AtomSelectionOptions;
  import ffx.potential.cli.WriteoutOptions;
  import ffx.realspace.cli.RealSpaceOptions;
  import ffx.utilities.FFXBinding;
  import ffx.xray.RefinementEnergy;
  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 ffx.utilities.TinkerUtils.version;
  
  /**
   * The Real Space Dynamics script.
   * <br>
   * Usage:
   * <br>
   * ffxc realspace.Dynamics [options] &lt;filename&gt;
   */
  @Command(description = " Molecular dynamics on a Real Space target.", name = "realspace.Dynamics")
  public class Dynamics extends AlgorithmsCommand {
  
    @Mixin
    private AtomSelectionOptions atomSelectionOptions;
  
    @Mixin
    private DynamicsOptions dynamicsOptions;
  
    @Mixin
    private RealSpaceOptions realSpaceOptions;
  
    @Mixin
    private WriteoutOptions writeoutOptions;
  
    /**
     * One or more filenames.
     */
    @Parameters(arity = "1..*", paramLabel = "files", description = "PDB and Real Space input files.")
    private List<String> filenames;
  
    private RefinementEnergy refinementEnergy;
  
    /**
     * Dynamics constructor.
     */
    public Dynamics() {
      super();
    }
  
    /**
     * Dynamics constructor that sets the command line arguments.
    * @param args Command line arguments.
    */
   public Dynamics(String[] args) {
     super(args);
   }
 
   /**
    * Dynamics constructor.
    * @param binding The Binding to use.
    */
   public Dynamics(FFXBinding binding) {
     super(binding);
   }
 
   @Override
   public Dynamics run() {
 
     if (!init()) {
       return this;
     }
 
     dynamicsOptions.init();
 
     String filename;
     if (filenames != null && !filenames.isEmpty()) {
       activeAssembly = algorithmFunctions.open(filenames.get(0));
       filename = filenames.get(0);
     } else if (activeAssembly == null) {
       logger.info(helpString());
       return this;
     } else {
       filename = activeAssembly.getFile().getAbsolutePath();
     }
     MolecularAssembly[] molecularAssemblies = new MolecularAssembly[]{activeAssembly};
 
     logger.info("\n Running Real Space Dynamics on " + filename);
 
     atomSelectionOptions.setActiveAtoms(activeAssembly);
 
     // Create the refinement target.
     refinementEnergy = realSpaceOptions.toRealSpaceEnergy(filenames, molecularAssemblies);
 
     // Beginning force field energy.
     algorithmFunctions.energy(activeAssembly);
 
     // Restart File
     File dyn = new File(FilenameUtils.removeExtension(filename) + ".dyn");
     if (!dyn.exists()) {
       dyn = null;
     }
 
     MolecularDynamics molDyn = dynamicsOptions.getDynamics(writeoutOptions, refinementEnergy, activeAssembly, algorithmListener);
     refinementEnergy.setThermostat(molDyn.getThermostat());
 
     // Reset velocities (ignored if a restart file is given)
     boolean initVelocities = true;
     molDyn.dynamic(dynamicsOptions.getSteps(), dynamicsOptions.getDt(), dynamicsOptions.getReport(),
         dynamicsOptions.getWrite(), dynamicsOptions.getTemperature(), initVelocities, dyn);
 
     // Final target function.
     algorithmFunctions.energy(activeAssembly);
 
     File file = version(new File(FilenameUtils.removeExtension(filename) + ".pdb"));
     algorithmFunctions.saveAsPDB(molecularAssemblies, file);
 
     return this;
   }
 
   @Override
   public List<Potential> getPotentials() {
     return refinementEnergy == null ? 
         Collections.emptyList() : 
         Collections.singletonList((Potential) refinementEnergy);
   }
 }