// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2024.
   //
   // 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
  // you are not obligated to do so. If you do not wish to do so, delete this
  // exception statement from your version.
  //
  // ******************************************************************************
  package ffx.algorithms.cli;
  
  import ffx.algorithms.AlgorithmListener;
  import ffx.algorithms.optimize.anneal.AnnealingSchedule;
  import ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule;
  import ffx.algorithms.optimize.anneal.SimulatedAnnealing;
  import ffx.numerics.Potential;
  import ffx.potential.MolecularAssembly;
  import picocli.CommandLine.ArgGroup;
  import picocli.CommandLine.Option;
  
  import java.io.File;
  import java.util.logging.Logger;
  
  import static java.lang.String.format;
  
  /**
   * Represents command line options for scripts that utilize simulated annealing.
   *
   * @author Michael J. Schnieders
   * @author Jacob M. Litman
   * @since 1.0
   */
  public class AnnealOptions {
  
    private static final Logger logger = Logger.getLogger(AnnealOptions.class.getName());
  
    /**
     * The ArgGroup keeps the AnnealOptionGroup together when printing help.
     */
    @ArgGroup(heading = "%n Simulated Annealing Options%n", validate = false)
    private final AnnealOptionGroup group = new AnnealOptionGroup();
  
    /**
     * Number of annealing windows.
     *
     * @return Returns the number of windows.
     */
    public int getWindows() {
      return group.windows;
    }
  
    /**
     * Creates a SimulatedAnnealing object.
     *
     * @param dynamicsOptions   Dynamics options to use.
     * @param molecularAssembly MolecularAssembly
     * @param potential         Potential
     * @param algorithmListener AlgorithmListener
     * @return SimulatedAnnealing
     */
    public SimulatedAnnealing createAnnealer(DynamicsOptions dynamicsOptions,
                                             MolecularAssembly molecularAssembly, Potential potential,
                                             AlgorithmListener algorithmListener) {
      return createAnnealer(dynamicsOptions, molecularAssembly, potential, algorithmListener, null);
    }
  
    /**
     * Creates a SimulatedAnnealing object.
     *
     * @param dynamicsOptions   Dynamics options to use.
     * @param molecularAssembly MolecularAssembly
    * @param potential         Potential
    * @param algorithmListener AlgorithmListener
    * @param dynFile           Dynamics restart file.
    * @return SimulatedAnnealing
    */
   public SimulatedAnnealing createAnnealer(DynamicsOptions dynamicsOptions, MolecularAssembly molecularAssembly,
                                            Potential potential, AlgorithmListener algorithmListener,
                                            File dynFile) {
     AnnealingSchedule schedule = getSchedule();
     double totNormLen = schedule.totalWindowLength();
     long totSteps = dynamicsOptions.getSteps();
     long perWindowSteps = (long) (totSteps / totNormLen);
 
     if (totSteps > perWindowSteps * totNormLen) {
       ++perWindowSteps;
     }
 
     long minWindowSteps = (long) (perWindowSteps * schedule.minWindowLength());
     long maxWindowSteps = (long) (perWindowSteps * schedule.maxWindowLength());
     int nWindows = schedule.getNumWindows();
 
     if (minWindowSteps == maxWindowSteps && minWindowSteps == perWindowSteps) {
       logger.info(format(" Each of %d simulated annealing windows will have %d steps each, for a "
           + "total duration of %d time-steps", nWindows, perWindowSteps, perWindowSteps * nWindows));
     } else {
       logger.info(format(" Each of %d simulated annealing windows will have %d-%d steps each, "
               + "with a \"normal\" length of %d steps, for a total duration of %d time-steps", nWindows,
           minWindowSteps, maxWindowSteps, perWindowSteps,
           (int) (perWindowSteps * schedule.totalWindowLength())));
     }
 
     if (nWindows < 201) {
       StringBuilder sb = new StringBuilder(
           "\n Simulated annealing windows [index,MD steps, temperature (K)]:\n [");
       for (int i = 0; i < nWindows; i++) {
         double len = schedule.windowLength(i);
         double temp = schedule.getTemperature(i);
         sb.append(format("[%d,%d,%10.4g]", (i + 1), (int) (len * perWindowSteps), temp));
         if (i == nWindows - 1) {
           sb.append("]\n");
         } else if (i % 10 == 9) {
           sb.append("\n");
         } else {
           sb.append(",");
         }
       }
       logger.info(sb.toString());
     } else {
       logger.info(" Skipping printout of window lengths/temperatures (max printout at 200 windows)");
     }
 
     return new SimulatedAnnealing(molecularAssembly, potential, algorithmListener,
         dynamicsOptions.thermostat, dynamicsOptions.integrator, schedule, perWindowSteps,
         dynamicsOptions.getDt(), isReinitVelocities(), dynFile);
   }
 
   /**
    * Constructs an AnnealingSchedule.
    *
    * @return An AnnealingSchedule.
    */
   public AnnealingSchedule getSchedule() {
     SimulatedAnnealing.Schedules schedules = SimulatedAnnealing.Schedules.parse(getTemperString());
     AnnealingSchedule annealingSchedule = schedules.generate(getWindows(), getLow(), getUpper());
     if (getTemperBefore() > 0 || getTemperAfter() > 0) {
       annealingSchedule = new FlatEndAnnealSchedule(annealingSchedule, getLow(), getUpper(),
           getTemperBefore(), getTemperAfter());
     }
     return annealingSchedule;
   }
 
   public void setWindows(int windows) {
     group.windows = windows;
   }
 
   /**
    * Low temperature limit in degrees Kelvin.
    *
    * @return Returns the low temperature limit.
    */
   public double getLow() {
     return group.low;
   }
 
   public void setLow(double low) {
     group.low = low;
   }
 
   /**
    * Upper temperature limit in degrees Kelvin.
    *
    * @return Returns the upper temperature limit.
    */
   public double getUpper() {
     return group.upper;
   }
 
   public void setUpper(double upper) {
     group.upper = upper;
   }
 
   /**
    * Forces simulated annealing to re-initialize velocities to the new temperature at each annealing
    * step, rather than letting the thermostat shift temperature downwards.
    *
    * @return Returns true for re-initialization of velocities.
    */
   public boolean isReinitVelocities() {
     return group.reinitVelocities;
   }
 
   public void setReinitVelocities(boolean reinitVelocities) {
     group.reinitVelocities = reinitVelocities;
   }
 
   /**
    * Sets the schedule to be used.
    *
    * @return Returns a String representation of the tempering schedule.
    */
   public String getTemperString() {
     return group.temperString;
   }
 
   public void setTemperString(String temperString) {
     group.temperString = temperString;
   }
 
   /**
    * Sets the number of annealing windows to hold flat at the high temperature (in addition to normal
    * windows).
    *
    * @return Returns the number of annealing windows to hold flat at the high temperature.
    */
   public int getTemperBefore() {
     return group.temperBefore;
   }
 
   public void setTemperBefore(int temperBefore) {
     group.temperBefore = temperBefore;
   }
 
   /**
    * Sets the number of annealing windows to hold flat at the low temperature (in addition to normal
    * windows).
    *
    * @return Returns the number of annealing windows to hold flat at the low temperature.
    */
   public int getTemperAfter() {
     return group.temperAfter;
   }
 
   public void setTemperAfter(int temperAfter) {
     group.temperAfter = temperAfter;
   }
 
   /**
    * Collection of Simulated Annealing Options.
    */
   private static class AnnealOptionGroup {
 
     /**
      * -w or --windows Number of annealing windows (10).
      */
     @Option(names = {"-W", "--windows"}, paramLabel = "10", defaultValue = "10",
         description = "Number of annealing windows.")
     private int windows = 10;
 
     /**
      * -l or --low Low temperature limit in degrees Kelvin (10.0).
      */
     @Option(names = {"--tl", "--temperatureLow"}, paramLabel = "10.0", defaultValue = "10.0",
         description = "Low temperature limit (Kelvin).")
     private double low = 10.0;
 
     /**
      * -u or --upper Upper temperature limit in degrees Kelvin (1000.0).
      */
     @Option(names = {"--tu", "--temperatureUpper"}, paramLabel = "1000.0", defaultValue = "1000.0",
         description = "High temperature limit (Kelvin).")
     private double upper = 1000.0;
 
     /**
      * --rv or --reinitVelocities forces simulated annealing to re-initialize velocities to the new
      * temperature at each annealing step, rather than letting the thermostat shift temperature
      * downwards.
      */
     @Option(names = {"--rv", "--reinitVelocities"}, paramLabel = "false", defaultValue = "false",
         description = "Re-initialize velocities before each round of annealing.")
     private boolean reinitVelocities = false;
 
     /**
      * --tmS or --temperingSchedule sets the schedule to be used.
      */
     @Option(names = {"--tmS", "--temperingSchedule"}, paramLabel = "EXP", defaultValue = "EXP",
         description = "Tempering schedule: choose between EXP (exponential) or LINEAR")
     private String temperString = "EXP";
 
     /**
      * --tmB or --temperingBefore sets the number of annealing windows to hold flat at the high
      * temperature (in addition to normal windows).
      */
     @Option(names = {"--tmB", "--temperingBefore"}, paramLabel = "0", defaultValue = "0",
         description = "Number of (annealing, not MD/MC) steps to remain at the high temperature")
     private int temperBefore = 0;
 
     /**
      * --tmA or --temperingAfter sets the number of annealing windows to hold flat at the low
      * temperature (in addition to normal windows).
      */
     @Option(names = {"--tmA", "--temperingAfter"}, paramLabel = "0", defaultValue = "0",
         description = "Number of (annealing, not MD/MC) steps to remain at the low temperature")
     private int temperAfter = 0;
   }
 }