//******************************************************************************
   //
   // 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
  // you are not obligated to do so. If you do not wish to do so, delete this
  // exception statement from your version.
  //
  //******************************************************************************
  package ffx.xray.commands;
  
  import ffx.algorithms.AlgorithmListener;
  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.utilities.FFXBinding;
  import ffx.xray.DiffractionData;
  import ffx.xray.RefinementEnergy;
  import ffx.xray.cli.XrayOptions;
  import ffx.xray.refine.RefinementMode;
  import org.apache.commons.configuration2.CompositeConfiguration;
  import org.apache.commons.io.FilenameUtils;
  import picocli.CommandLine.Command;
  import picocli.CommandLine.Mixin;
  import picocli.CommandLine.Option;
  import picocli.CommandLine.Parameters;
  
  import java.io.File;
  import java.util.Collections;
  import java.util.List;
  
  /**
   * The X-ray Dynamics script.
   * <br>
   * Usage:
   * <br>
   * ffxc xray.Dynamics [options] &lt;filename&gt;
   */
  @Command(description = " Run Dynamics on an X-ray target.", name = "xray.Dynamics")
  public class Dynamics extends AlgorithmsCommand implements AlgorithmListener {
  
    @Mixin
    private XrayOptions xrayOptions;
  
    @Mixin
    private DynamicsOptions dynamicsOptions;
  
    @Mixin
    AtomSelectionOptions atomSelectionOptions;
  
    @Mixin
    private WriteoutOptions writeoutOptions;
  
    /**
     * --mtz Write out MTZ containing structure factor coefficients.
     */
    @Option(names = {"--mtz"}, paramLabel = "false",
        description = "Write out an MTZ containing structure factor coefficients.")
    private boolean mtz = false;
  
    /**
     * One or more filenames.
     */
    @Parameters(arity = "1..*", paramLabel = "files", description = "PDB and Diffraction input files.")
    private List<String> filenames;
  
    private MolecularAssembly[] molecularAssemblies;
   private DiffractionData diffractionData;
   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();
     xrayOptions.init();
 
     String filename;
     if (filenames != null && !filenames.isEmpty()) {
       // Each alternate conformer is returned in a separate MolecularAssembly.
       molecularAssemblies = algorithmFunctions.openAll(filenames.getFirst());
       activeAssembly = molecularAssemblies[0];
     } else if (activeAssembly == null) {
       logger.info(helpString());
       return this;
     } else {
       molecularAssemblies = new MolecularAssembly[]{activeAssembly};
     }
 
     // Update the active filename
     filename = activeAssembly.getFile().getAbsolutePath();
 
     // Apply active atom flags.
     for (MolecularAssembly molecularAssembly : molecularAssemblies) {
       atomSelectionOptions.setActiveAtoms(molecularAssembly);
     }
 
     logger.info("\n Running xray.Dynamics on " + filename);
 
     // Combine script flags (in parseResult) with properties.
     CompositeConfiguration properties = activeAssembly.getProperties();
     xrayOptions.setProperties(parseResult, properties);
 
     // Set up diffraction data (can be multiple files)
     diffractionData = xrayOptions.getDiffractionData(filenames, molecularAssemblies, properties);
     refinementEnergy = xrayOptions.toXrayEnergy(diffractionData);
 
     // Log the energy of each MolecularAssembly
     algorithmFunctions.energy(molecularAssemblies);
 
     // Restart is currently only supported for COORDINATES mode.
     File dyn = null;
     if (xrayOptions.refinementMode == RefinementMode.COORDINATES) {
       dyn = new File(FilenameUtils.removeExtension(filename) + ".dyn");
       if (!dyn.exists()) {
         dyn = null;
       }
     }
 
     MolecularDynamics molecularDynamics = dynamicsOptions.getDynamics(writeoutOptions,
         refinementEnergy, activeAssembly, this);
     refinementEnergy.setThermostat(molecularDynamics.getThermostat());
     boolean initVelocities = true;
     molecularDynamics.dynamic(dynamicsOptions.getSteps(), dynamicsOptions.getDt(), dynamicsOptions.getReport(),
         dynamicsOptions.getWrite(), dynamicsOptions.getTemperature(), initVelocities, dyn);
 
     // Print the final refinement statistics.
     diffractionData.scaleBulkFit();
     diffractionData.printStats();
 
     // Print the final energy of each conformer.
     algorithmFunctions.energy(molecularAssemblies);
 
     logger.info(" ");
     diffractionData.writeModel(FilenameUtils.removeExtension(filename) + ".pdb");
 
     if (mtz) {
       diffractionData.writeData(FilenameUtils.removeExtension(filename) + ".mtz");
     }
 
     return this;
   }
 
   @Override
   public List<Potential> getPotentials() {
     return getPotentialsFromAssemblies(molecularAssemblies);
   }
 
   @Override
   public boolean destroyPotentials() {
     return diffractionData == null ? true : diffractionData.destroy();
   }
 
   @Override
   public boolean algorithmUpdate(MolecularAssembly active) {
     logger.info(" R/Rfree " + diffractionData.printOptimizationUpdate());
     return true;
   }
 }