//******************************************************************************
   //
   // 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.potential.commands;
  
  import ffx.numerics.Potential;
  import ffx.potential.ForceFieldEnergy;
  import ffx.potential.cli.PotentialCommand;
  import ffx.potential.cli.TimerOptions;
  import ffx.utilities.FFXBinding;
  import picocli.CommandLine.Command;
  import picocli.CommandLine.Mixin;
  import picocli.CommandLine.Parameters;
  
  import java.util.ArrayList;
  import java.util.Collections;
  import java.util.List;
  
  import static java.lang.String.format;
  import static org.apache.commons.math3.util.FastMath.sqrt;
  
  /**
   * The Timer command evaluates the wall clock time for energy and forces.
   *
   * Usage:
   *   ffxc Timer [options] <filename>
   */
  @Command(name = "Timer", description = " Time energy evaluations.")
  public class Timer extends PotentialCommand {
  
    /** Mix in timing options. */
    @Mixin
    private TimerOptions timer = new TimerOptions();
  
    /** The final argument is an atomic coordinate file in PDB or XYZ format. */
    @Parameters(arity = "1", paramLabel = "file",
        description = "The atomic coordinate file in PDB or XYZ format.")
    private String filename = null;
  
    private ForceFieldEnergy energy = null;
  
    public Timer() { super(); }
    public Timer(FFXBinding binding) { super(binding); }
    public Timer(String[] args) { super(args); }
  
    @Override
    public Timer run() {
      // Init the context and bind variables.
      if (!init()) {
        return this;
      }
  
      // Set the number of threads.
      if (timer.getThreads() > 0) {
        System.setProperty("pj.nt", Integer.toString(timer.getThreads()));
      }
  
      // Load the MolecularAssembly.
      activeAssembly = getActiveAssembly(filename);
      if (activeAssembly == null) {
        logger.info(helpString());
        return this;
      }
  
      // Set the filename.
     filename = activeAssembly.getFile().getAbsolutePath();
 
     if (timer.getNoGradient()) {
       logger.info("\n Timing energy for " + filename);
     } else {
       logger.info("\n Timing energy and gradient for " + filename);
     }
 
     int nEvals = timer.getIterations(); // The number of iterations.
 
     energy = activeAssembly.getPotentialEnergy();
 
     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 = energy.energy(!timer.getNoGradient(), timer.getVerbose());
       time += System.nanoTime();
       if (!timer.getVerbose()) {
         logger.info(format(" %4d Energy %16.8f in %6.3f (sec)", i, e, time * 1.0E-9));
       }
       minTime = Math.min(time, minTime);
       if (i >= (nEvals / 2)) {
         double time2 = time * 1.0E-9;
         sumTime2 += (time2 * time2);
       }
     }
 
     ++halfnEvals;
     double rmsTime = 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() {
     if (energy == null) {
       return Collections.emptyList();
     } else {
       List<Potential> list = new ArrayList<>(1);
       list.add(energy);
       return list;
     }
   }
 }