//******************************************************************************
   //
   // 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.
   //
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  package ffx.algorithms.commands;
  
  import ffx.algorithms.cli.AlgorithmsCommand;
  import ffx.algorithms.cli.MinimizeOptions;
  import ffx.algorithms.optimize.CrystalMinimize;
  import ffx.algorithms.optimize.Minimize;
  import ffx.numerics.Potential;
  import ffx.potential.ForceFieldEnergy;
  import ffx.potential.MolecularAssembly.FractionalMode;
  import ffx.potential.XtalEnergy;
  import ffx.potential.cli.AtomSelectionOptions;
  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.Option;
  import picocli.CommandLine.Parameters;
  
  import java.io.File;
  import java.util.Collections;
  import java.util.List;
  
  import static java.lang.String.format;
  import static org.apache.commons.math3.util.FastMath.abs;
  
  /**
   * The MinimizeCrystals script uses a limited-memory BFGS algorithm to minimize the
   * energy of a crystal, including both coordinates and unit cell parameters.
   * <br>
   * Usage:
   * <br>
   * ffxc MinimizeCrystals [options] &lt;filename&gt;
   */
  @Command(description = " Minimize crystal unit cell parameters.", name = "MinimizeCrystals")
  public class MinimizeCrystals extends AlgorithmsCommand {
  
    @Mixin
    private MinimizeOptions minimizeOptions;
  
    @Mixin
    private AtomSelectionOptions atomSelectionOptions;
  
    /**
     * -c or --coords to cycle between lattice and coordinate optimization until both satisfy the convergence criteria.
     */
    @Option(names = {"-c", "--coords"}, paramLabel = "false", defaultValue = "false",
        description = "Cycle between lattice and coordinate optimization instead of optimizing both together.")
    private boolean coords;
  
    /**
     * -f or --fractional to set the optimization to maintain fractional coordinates [ATOM/MOLECULE/OFF].
     */
    @Option(names = {"-f", "--fractional"}, paramLabel = "OFF", defaultValue = "OFF",
        description = "Maintain fractional coordinates during lattice optimization [OFF/MOLECULE/ATOM].")
    private String fractional;
  
    /**
     * -t or --tensor to print out partial derivatives of the energy with respect to unit cell parameters.
    */
   @Option(names = {"-t", "--tensor"}, paramLabel = "false", defaultValue = "false",
       description = "Compute partial derivatives of the energy with respect to unit cell parameters.")
   private boolean tensor;
 
   /**
    * --et or --energyTolerance End minimization if new energy deviates less than this tolerance.
    */
   @Option(names = {"--et", "--energyTolerance"}, paramLabel = "1.0e-10", defaultValue = "1.0e-10",
       description = "End minimization if new energy deviates less than this tolerance.")
   private double tolerance;
 
   /**
    * --mi or --minimumIterations End minimization if fewer iterations were taken for both coordinate and lattice minimization.
    */
   @Option(names = {"--mi", "--minimumIterations"}, paramLabel = "-1", defaultValue = "-1",
       description = "End minimization if it starts to cycle between small coordinate and lattice parameter fluctuations.")
   private int minIterations;
 
   /**
    * --cy or --cycles End minimization if it has cycled between lattice parameters and coordinates more than this value.
    */
   @Option(names = {"--cy", "--cycles"}, paramLabel = "-1", defaultValue = "-1",
       description = "End minimization if it has cycled between lattice parameters and coordinates more than this value.")
   private int cycles;
 
   /**
    * The final argument(s) should be an XYZ or PDB filename.
    */
   @Parameters(arity = "1", paramLabel = "file", description = "Atomic coordinate files in PDB or XYZ format.")
   private String filename = null;
 
   private XtalEnergy xtalEnergy;
   private CrystalMinimize crystalMinimize;
 
   /**
    * CrystalMin Constructor.
    */
   public MinimizeCrystals() {
     super();
   }
 
   /**
    * CrystalMin Constructor.
    *
    * @param binding The Binding to use.
    */
   public MinimizeCrystals(FFXBinding binding) {
     super(binding);
   }
 
   /**
    * MinimizeCrystals constructor that sets the command line arguments.
    *
    * @param args Command line arguments.
    */
   public MinimizeCrystals(String[] args) {
     super(args);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public MinimizeCrystals run() {
 
     // Init the context and bind variables.
     if (!init()) {
       return this;
     }
 
     // Load the MolecularAssembly.
     activeAssembly = getActiveAssembly(filename);
     if (activeAssembly == null) {
       logger.info(helpString());
       return this;
     }
 
     // Set the filename
     filename = activeAssembly.getFile().getAbsolutePath();
 
     logger.info("\n Running CrystalMinimize on " + filename);
     logger.info("\n RMS gradient convergence criteria: " + minimizeOptions.getEps());
 
     atomSelectionOptions.setActiveAtoms(activeAssembly);
 
     ForceFieldEnergy forceFieldEnergy = activeAssembly.getPotentialEnergy();
     xtalEnergy = new XtalEnergy(forceFieldEnergy, activeAssembly, coords);
     xtalEnergy.setFractionalCoordinateMode(FractionalMode.MOLECULE);
     SystemFilter systemFilter = algorithmFunctions.getFilter();
 
     // Apply fractional coordinate mode.
     if (fractional != null && !fractional.isEmpty()) {
       try {
         FractionalMode mode = FractionalMode.valueOf(fractional.toUpperCase());
         xtalEnergy.setFractionalCoordinateMode(mode);
       } catch (Exception ignored) {
         logger.info(" Unrecognized fractional coordinate mode: " + fractional);
         logger.info(" Fractional coordinate mode is set to MOLECULE.");
       }
     }
 
     runMinimize();
 
     if (tensor) {
       crystalMinimize.printTensor();
     }
 
     // Handle Single Topology Cases.
     if (baseDir == null || !baseDir.exists() || !baseDir.isDirectory() || !baseDir.canWrite()) {
       baseDir = new File(FilenameUtils.getFullPath(filename));
     }
 
     String dirName = baseDir.toString() + File.separator;
     String name = FilenameUtils.getName(filename);
     String ext = FilenameUtils.getExtension(name);
     name = FilenameUtils.removeExtension(name);
     File saveFile;
     PDBFilter pdbFilter = null;
     XYZFilter xyzFilter = null;
 
     if (ext.toUpperCase().contains("XYZ")) {
       saveFile = new File(dirName + name + ".xyz");
       xyzFilter = new XYZFilter(saveFile, activeAssembly, activeAssembly.getForceField(),
           activeAssembly.getProperties());
       algorithmFunctions.saveAsXYZ(activeAssembly, saveFile);
     } else if (ext.toUpperCase().contains("ARC")) {
       saveFile = new File(dirName + name + ".arc");
       saveFile = algorithmFunctions.versionFile(saveFile);
       xyzFilter = new XYZFilter(saveFile, activeAssembly, activeAssembly.getForceField(),
           activeAssembly.getProperties());
       algorithmFunctions.saveAsXYZ(activeAssembly, saveFile);
     } else {
       saveFile = new File(dirName + name + ".pdb");
       saveFile = algorithmFunctions.versionFile(saveFile);
       pdbFilter = new PDBFilter(saveFile, activeAssembly, activeAssembly.getForceField(),
           activeAssembly.getProperties());
       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()) {
         if (systemFilter instanceof PDBFilter) {
           FileUtils.append(saveFile, "ENDMDL\n");
           runMinimize();
           pdbFilter.writeFile(saveFile, true, false, false);
         } else if (systemFilter instanceof XYZFilter) {
           runMinimize();
           xyzFilter.writeFile(saveFile, true);
         }
       }
 
       if (systemFilter instanceof PDBFilter) {
         FileUtils.append(saveFile, "END\n");
       }
     }
 
     return this;
   }
 
   private void runMinimize() {
     logger.info("\n Crystal Minimizing " + activeAssembly.getName());
     crystalMinimize = new CrystalMinimize(activeAssembly, xtalEnergy, algorithmListener);
     crystalMinimize.minimize(minimizeOptions.getNBFGS(), minimizeOptions.getEps(), minimizeOptions.getIterations());
     logger.info("\n Crystal Minimization Complete.");
     double energy = crystalMinimize.getEnergy();
 
     // Complete rounds of coordinate and lattice optimization.
     if (coords) {
       ForceFieldEnergy forceFieldEnergy = activeAssembly.getPotentialEnergy();
       Minimize minimize = new Minimize(activeAssembly, forceFieldEnergy, algorithmListener);
       int numCycles = 0;
       while (true) {
         // Complete a round of coordinate optimization.
         minimize.minimize(minimizeOptions.getNBFGS(), minimizeOptions.getEps(), minimizeOptions.getIterations());
         double newEnergy = minimize.getEnergy();
         int status = minimize.getStatus();
         if (status != 0) {
           break;
         }
         if (abs(newEnergy - energy) <= tolerance) {
           break;
         }
         energy = newEnergy;
 
         // Complete a round of lattice optimization.
         crystalMinimize.minimize(minimizeOptions.getNBFGS(), minimizeOptions.getEps(), minimizeOptions.getIterations());
         newEnergy = crystalMinimize.getEnergy();
         status = crystalMinimize.getStatus();
         if (status != 0) {
           break;
         }
         if (abs(newEnergy - energy) <= tolerance) {
           break;
         }
         energy = newEnergy;
         if (minIterations > 0) {
           int coordIters = minimize.getIterations();
           int latticeIters = crystalMinimize.getIterations();
           if (coordIters < minIterations && latticeIters < minIterations) {
             // Prevent looping between similar structures (i.e., A-min to->B, B-min to->A)
             logger.info(format(" Current iteration (coords: %3d, lattice: %3d) has exceeded maximum allowable iterations (%3d).", coordIters, latticeIters, minIterations));
             break;
           }
         }
         // Minimization has cycled between lattice and coords. Therefore increase number of cycles and check if done.
         if (cycles > 0 && ++numCycles >= cycles) {
           logger.info(format(" Current cycle (%3d) has exceeded maximum allowable cycles (%3d).", numCycles, cycles));
           break;
         }
       }
     }
     updateTitle(energy);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public List<Potential> getPotentials() {
     List<Potential> potentials;
     if (xtalEnergy == null) {
       potentials = Collections.emptyList();
     } else {
       potentials = Collections.singletonList((Potential) xtalEnergy);
     }
     return potentials;
   }
 
 }