//******************************************************************************
   //
   // 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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  // module which is not derived from or based on this library. If you modify this
  // library, you may extend this exception to your version of the library, but
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  // exception statement from your version.
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  //******************************************************************************
  package ffx.xray.commands;
  
  import ffx.algorithms.cli.AlgorithmsCommand;
  import ffx.numerics.Potential;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.cli.AtomSelectionOptions;
  import ffx.potential.cli.TimerOptions;
  import ffx.utilities.FFXBinding;
  import ffx.xray.DiffractionData;
  import ffx.xray.RefinementEnergy;
  import ffx.xray.cli.XrayOptions;
  import org.apache.commons.configuration2.CompositeConfiguration;
  import picocli.CommandLine.Command;
  import picocli.CommandLine.Mixin;
  import picocli.CommandLine.Parameters;
  
  import java.util.List;
  
  import static java.lang.String.format;
  
  /**
   * The X-ray Timer script.
   * <br>
   * Usage:
   * <br>
   * ffxc xray.Timer [options] &lt;filename&gt;
   */
  @Command(description = " Time calculation of the X-ray target.", name = "xray.Timer")
  public class Timer extends AlgorithmsCommand {
  
    @Mixin
    private TimerOptions timerOptions;
  
    @Mixin
    private XrayOptions xrayOptions;
  
    @Mixin
    AtomSelectionOptions atomSelectionOptions;
  
    /**
     * One or more filenames.
     */
    @Parameters(arity = "1..*", paramLabel = "files", description = "PDB and Diffraction input files.")
    private List<String> filenames;
  
    private DiffractionData diffractionData;
    private MolecularAssembly[] molecularAssemblies;
  
    private RefinementEnergy refinementEnergy;
  
    /**
     * Timer constructor.
     */
    public Timer() {
      super();
    }
  
    /**
     * Timer constructor that sets the command line arguments.
     *
     * @param args Command line arguments.
     */
   public Timer(String[] args) {
     super(args);
   }
 
   /**
    * Timer constructor.
    *
    * @param binding The Binding to use.
    */
   public Timer(FFXBinding binding) {
     super(binding);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public Timer run() {
 
     if (!init()) {
       return this;
     }
 
     xrayOptions.init();
 
     // Set the number of threads (needs to be done before opening the files).
     if (timerOptions.getThreads() > 0) {
       System.setProperty("pj.nt", Integer.toString(timerOptions.getThreads()));
     }
 
     String filename;
     if (filenames != null && !filenames.isEmpty()) {
       // Each alternate conformer is returned in a separate MolecularAssembly.
       molecularAssemblies = algorithmFunctions.openAll(filenames.get(0));
       activeAssembly = molecularAssemblies[0];
       filename = filenames.get(0);
     } else if (activeAssembly == null) {
       logger.info(helpString());
       return this;
     } else {
       molecularAssemblies = new MolecularAssembly[]{activeAssembly};
       filename = activeAssembly.getFile().getAbsolutePath();
     }
 
     logger.info("\n Running xray.Timer on " + filename);
 
     // Apply active atom flags.
     for (MolecularAssembly molecularAssembly : molecularAssemblies) {
       atomSelectionOptions.setActiveAtoms(molecularAssembly);
     }
 
     // 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);
 
     // Print the initial energy of each conformer.
     algorithmFunctions.energy(molecularAssemblies);
 
     int n = refinementEnergy.getNumberOfVariables();
     double[] x = new double[n];
     double[] g = new double[n];
     refinementEnergy.getCoordinates(x);
     Potential energy = refinementEnergy.getDataEnergy();
 
     logger.info("\n Beginning Timings\n");
 
     int nEvals = timerOptions.getIterations();
     boolean gradient = !timerOptions.getNoGradient();
     long minTime = Long.MAX_VALUE;
     double sumTime2 = 0.0;
     int halfnEvals = (nEvals % 2 == 1) ? (nEvals / 2) : (nEvals / 2) - 1; // Halfway point
     for (int i = 0; i < nEvals; i++) {
       long time = -System.nanoTime();
       double e;
       if (gradient) {
         e = energy.energyAndGradient(x, g);
       } else {
         e = energy.energy(x);
       }
       time += System.nanoTime();
       if (gradient) {
         logger.info(format(" Energy & Gradient: %12.6f in %6.3f (sec)", e, time * 1.0E-9));
       } else {
         logger.info(format(" Energy: %12.6f in %6.3f (sec)", e, time * 1.0E-9));
       }
 
       minTime = time < minTime ? time : minTime;
       if (i >= nEvals / 2) {
         double time2 = time * 1.0E-9;
         sumTime2 += (time2 * time2);
       }
     }
 
     ++halfnEvals;
     double rmsTime = Math.sqrt(sumTime2 / halfnEvals);
     logger.info(format("\n Minimum time:           %6.3f (sec)", minTime * 1.0E-9));
     logger.info(format(" RMS time (latter half): %6.3f (sec)", rmsTime));
 
     return this;
   }
 
   @Override
   public List<Potential> getPotentials() {
     return getPotentialsFromAssemblies(molecularAssemblies);
   }
 
   @Override
   public boolean destroyPotentials() {
     return diffractionData == null ? true : diffractionData.destroy();
   }
 }