//******************************************************************************
   //
   // 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
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  // details.
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  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
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  // combined work based on this library. Thus, the terms and conditions of the
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  // permission to link this library with independent modules to produce an
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  package ffx.algorithms.commands;
  
  import ffx.algorithms.cli.AlgorithmsCommand;
  import ffx.algorithms.cli.MinimizeOptions;
  import ffx.crystal.Crystal;
  import ffx.numerics.Potential;
  import ffx.potential.ForceFieldEnergy;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.bonded.LambdaInterface;
  import ffx.potential.cli.AlchemicalOptions;
  import ffx.potential.cli.AtomSelectionOptions;
  import ffx.potential.cli.TopologyOptions;
  import ffx.potential.parsers.PDBFilter;
  import ffx.potential.parsers.SystemFilter;
  import ffx.potential.parsers.XYZFilter;
  import ffx.utilities.FFXBinding;
  import ffx.utilities.FileUtils;
  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.ArrayList;
  import java.util.Collections;
  import java.util.List;
  
  import static java.lang.String.format;
  
  /**
   * The Minimize script uses a limited-memory BFGS algorithm to minimize the energy of a molecular system.
   * <br>
   * Usage:
   * <br>
   * ffxc Minimize [options] &lt;filename&gt; [file2...]
   */
  @Command(description = " Run L-BFGS minimization on a system.", name = "Minimize")
  public class Minimize extends AlgorithmsCommand {
  
    @Mixin
    private MinimizeOptions minimizeOptions;
  
    @Mixin
    private AtomSelectionOptions atomSelectionOptions;
  
    @Mixin
    private AlchemicalOptions alchemicalOptions;
  
    @Mixin
    private TopologyOptions topologyOptions;
  
    /**
     * The final argument(s) should be one or more filenames.
     */
    @Parameters(arity = "1..*", paramLabel = "files", description = "Atomic coordinate files in PDB or XYZ format.")
    private List<String> filenames = null;
  
    private MolecularAssembly[] topologies;
    private Potential potential;
  
    /**
     * The minimization algorithm.
    */
   private ffx.algorithms.optimize.Minimize minimize;
 
   /**
    * Minimize Constructor.
    */
   public Minimize() {
     super();
   }
 
   /**
    * Minimize Constructor.
    *
    * @param binding The Binding to use.
    */
   public Minimize(FFXBinding binding) {
     super(binding);
   }
 
   /**
    * Minimize constructor that sets the command line arguments.
    *
    * @param args Command line arguments.
    */
   public Minimize(String[] args) {
     super(args);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public Minimize run() {
 
     if (!init()) {
       return this;
     }
 
     // Determine the number of topologies to be read and allocate the array.
     int numTopologies = topologyOptions.getNumberOfTopologies(filenames);
     int threadsPerTopology = topologyOptions.getThreadsPerTopology(numTopologies);
     topologies = new MolecularAssembly[numTopologies];
 
     // Turn on computation of lambda derivatives if softcore atoms exist.
     alchemicalOptions.setAlchemicalProperties();
     topologyOptions.setAlchemicalProperties(numTopologies);
 
     // Read in files.
     if (filenames == null || filenames.isEmpty()) {
       activeAssembly = getActiveAssembly(null);
       if (activeAssembly == null) {
         logger.info(helpString());
         return this;
       }
       filenames = new ArrayList<>();
       filenames.add(activeAssembly.getFile().getName());
       topologies[0] = alchemicalOptions.processFile(topologyOptions, activeAssembly, 0);
     } else {
       logger.info(format(" Initializing %d topologies...", numTopologies));
       for (int i = 0; i < numTopologies; i++) {
         topologies[i] = alchemicalOptions.openFile(algorithmFunctions,
             topologyOptions, threadsPerTopology, filenames.get(i), i);
       }
       activeAssembly = topologies[0];
     }
 
     if (topologies.length == 1) {
       atomSelectionOptions.setActiveAtoms(topologies[0]);
     }
 
     // Configure the potential to test.
     StringBuilder sb = new StringBuilder("\n Minimizing energy of ");
     potential = topologyOptions.assemblePotential(topologies, sb);
     logger.info(sb.toString());
 
     LambdaInterface linter = (potential instanceof LambdaInterface) ? (LambdaInterface) potential : null;
     if (linter != null) {
       linter.setLambda(alchemicalOptions.getInitialLambda());
     }
 
     SystemFilter systemFilter = algorithmFunctions.getFilter();
 
     double[] x = new double[potential.getNumberOfVariables()];
     potential.getCoordinates(x);
     potential.energy(x, true);
 
     minimize = new ffx.algorithms.optimize.Minimize(topologies[0], potential, algorithmListener);
     minimize.minimize(minimizeOptions.getNBFGS(), minimizeOptions.getEps(), minimizeOptions.getIterations());
 
     potential.getCoordinates(x);
     activeAssembly = systemFilter.getActiveMolecularSystem();
     updateTitle(potential.energy(x, true));
     if (topologies.length > 1) {
       // Handle Multiple Topology Cases.
       for (MolecularAssembly molecularAssembly : topologies) {
         String modelFilename = molecularAssembly.getFile().getAbsolutePath();
 
         if (baseDir == null || !baseDir.exists() || !baseDir.isDirectory() || !baseDir.canWrite()) {
           baseDir = new File(FilenameUtils.getFullPath(modelFilename));
         }
 
         String dirName = baseDir.toString() + File.separator;
         String fileName = FilenameUtils.getName(modelFilename);
         String ext = FilenameUtils.getExtension(fileName);
         fileName = FilenameUtils.removeExtension(fileName);
 
         if (ext.toUpperCase().contains("XYZ")) {
           algorithmFunctions.saveAsXYZ(molecularAssembly, new File(dirName + fileName + ".xyz"));
         } else {
           algorithmFunctions.saveAsPDB(molecularAssembly, new File(dirName + fileName + ".pdb"));
         }
       }
     } else {
       // Handle Single Topology Cases.
       setActiveAssembly(topologies[0]);
       String modelFilename = activeAssembly.getFile().getAbsolutePath();
       if (baseDir == null || !baseDir.exists() || !baseDir.isDirectory() || !baseDir.canWrite()) {
         baseDir = new File(FilenameUtils.getFullPath(modelFilename));
       }
 
       String dirName = baseDir.toString() + File.separator;
       String fileName = FilenameUtils.getName(modelFilename);
       String ext = FilenameUtils.getExtension(fileName);
       fileName = FilenameUtils.removeExtension(fileName);
       File saveFile;
       SystemFilter writeFilter;
       if (ext.toUpperCase().contains("XYZ")) {
         saveFile = new File(dirName + fileName + ".xyz");
         writeFilter = new XYZFilter(saveFile, activeAssembly, activeAssembly.getForceField(),
             activeAssembly.getProperties());
         algorithmFunctions.saveAsXYZ(activeAssembly, saveFile);
       } else if (ext.toUpperCase().contains("ARC")) {
         saveFile = new File(dirName + fileName + ".arc");
         saveFile = algorithmFunctions.versionFile(saveFile);
         writeFilter = new XYZFilter(saveFile, activeAssembly, activeAssembly.getForceField(),
             activeAssembly.getProperties());
         algorithmFunctions.saveAsXYZ(activeAssembly, saveFile);
       } else {
         saveFile = new File(dirName + fileName + ".pdb");
         saveFile = algorithmFunctions.versionFile(saveFile);
         PDBFilter pdbFilter = new PDBFilter(saveFile, activeAssembly, activeAssembly.getForceField(),
             activeAssembly.getProperties());
         writeFilter = pdbFilter;
         int numModels = systemFilter.countNumModels();
         if (numModels > 1) {
           pdbFilter.setModelNumbering(0);
         }
         pdbFilter.writeFile(saveFile, true, false, false);
       }
 
       if (systemFilter instanceof XYZFilter || systemFilter instanceof PDBFilter) {
         while (systemFilter.readNext()) {
           Crystal crystal = activeAssembly.getCrystal();
           ForceFieldEnergy forceFieldEnergy = activeAssembly.getPotentialEnergy();
           forceFieldEnergy.setCrystal(crystal);
           if (systemFilter instanceof PDBFilter) {
             FileUtils.append(saveFile, "ENDMDL\n");
             minimize.minimize(minimizeOptions.getEps(), minimizeOptions.getIterations());
             PDBFilter pdbFilter = (PDBFilter) systemFilter;
             pdbFilter.writeFile(saveFile, true, false, false);
           } else if (systemFilter instanceof XYZFilter) {
             minimize.minimize(minimizeOptions.getEps(), minimizeOptions.getIterations());
             writeFilter.writeFile(saveFile, true);
           }
         }
         if (systemFilter instanceof PDBFilter) {
           FileUtils.append(saveFile, "END\n");
         }
       }
     }
 
     return this;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public String toString() {
     StringBuilder sb = new StringBuilder();
     if (minimize != null) {
       sb.append(minimize.toString());
     } else {
       sb.append("No minimization has been performed.");
     }
     return sb.toString();
   }
 
   /**
    * Get the list of energies recorded during minimization.
    *
    * @return A List of Double energies, or null if minimization was not run.
    */
   public List<Double> getEnergyList() {
     if (minimize != null) {
       return minimize.getEnergyList();
     }
     return null;
   }
 
   /**
    * Get the final RMS gradient after minimization.
    *
    * @return The final RMS gradient or NaN if minimization was not run.
    */
   public double getRMSGradient() {
     if (minimize != null) {
       return minimize.getRMSGradient();
     }
     return Double.NaN;
   }
 
   /**
    * Get the final energy after minimization.
    *
    * @return The final energy or NaN if minimization was not run.
    */
   public double getEnergy() {
     if (minimize != null) {
       return minimize.getEnergy();
     }
     return Double.NaN;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public List<Potential> getPotentials() {
     List<Potential> potentials;
     if (potential == null) {
       potentials = Collections.emptyList();
     } else {
       potentials = Collections.singletonList(potential);
     }
     return potentials;
   }
 
 }