//******************************************************************************
   //
   // 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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  //******************************************************************************
  package ffx.potential.commands.test;
  
  import ffx.numerics.Potential;
  import ffx.potential.ForceFieldEnergy;
  import ffx.potential.cli.AtomSelectionOptions;
  import ffx.potential.cli.GradientOptions;
  import ffx.potential.cli.PotentialCommand;
  import ffx.potential.utils.GradientUtils;
  import ffx.utilities.FFXBinding;
  import picocli.CommandLine.Command;
  import picocli.CommandLine.Mixin;
  import picocli.CommandLine.Parameters;
  
  import java.util.Collections;
  import java.util.List;
  
  /**
   * The Gradient script evaluates the consistency of the energy and gradient.
   * <br>
   * Usage:
   * <br>
   * ffxc test.Gradient [options] &lt;filename&gt;
   */
  @Command(description = " Test the potential energy gradient.", name = "test.Gradient")
  public class Gradient extends PotentialCommand {
  
    @Mixin
    AtomSelectionOptions atomSelectionOptions;
  
    @Mixin
    GradientOptions gradientOptions;
  
    /**
     * The final argument is a single filename in PDB or XYZ format.
     */
    @Parameters(arity = "1", paramLabel = "file", description = "A PDB or XYZ coordinate file.")
    String filename = null;
  
    private ForceFieldEnergy energy;
    public int nFailures = 0;
  
    /**
     * Gradient constructor.
     */
    public Gradient() {
      super();
    }
  
    /**
     * Gradient constructor.
     * @param binding The Binding to use.
     */
    public Gradient(FFXBinding binding) {
      super(binding);
    }
  
    /**
     * Gradient constructor that sets the command line arguments.
     * @param args Command line arguments.
     */
    public Gradient(String[] args) {
      super(args);
   }
 
   /**
    * Execute the script.
    */
   @Override
   public Gradient 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 Testing the atomic coordinate gradient of " + filename + "\n");
 
     // Apply atom selections
     atomSelectionOptions.setActiveAtoms(activeAssembly);
 
     energy = activeAssembly.getPotentialEnergy();
     GradientUtils gradientUtils = new GradientUtils(energy);
     nFailures = gradientUtils.testGradient(gradientOptions);
     return this;
   }
 
   @Override
   public List<Potential> getPotentials() {
     List<Potential> potentials;
     if (energy == null) {
       potentials = Collections.emptyList();
     } else {
       potentials = Collections.singletonList(energy);
     }
     return potentials;
   }
 
 }