// ******************************************************************************
   //
   // 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
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  // provided that you also meet, for each linked independent module, the terms
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  // ******************************************************************************
  package ffx.algorithms.cli;
  
  import static java.lang.Double.parseDouble;
  import static java.lang.Integer.parseInt;
  import static java.lang.String.format;
  
  import ffx.algorithms.dynamics.Barostat;
  import ffx.crystal.CrystalPotential;
  import ffx.potential.MolecularAssembly;
  
  import java.util.logging.Logger;
  
  import picocli.CommandLine.ArgGroup;
  import picocli.CommandLine.Option;
  
  /**
   * Represents command line options for scripts that use a barostat/NPT.
   *
   * @author Michael J. Schnieders
   * @author Hernan V. Bernabe
   * @since 1.0
   */
  public class BarostatOptions {
  
    /**
     * Default maximum density constraint on the barostat that prevents reduction in unit cell
     * (particularly at or near vapor states).
     */
    public static final String DEFAULT_MAX_DENSITY = "1.6";
    /**
     * Default "tin box" constraint on the barostat that prevents expansion of the unit cell
     * (particularly at or near vapor states).
     */
    public static final String DEFAULT_MIN_DENSITY = "0.75";
    /**
     * Default width of proposed crystal angle moves (uniformly distributed) in degrees.
     */
    public static final String DEFAULT_MAX_ANGLE_MOVE = "0.5";
    /**
     * Default size of proposed unit cell volume moves (uniformly distributed) in Angstroms^3.
     */
    public static final String DEFAULT_MAX_VOLUME_MOVE = "1.0";
    /**
     * Default mean number of MD steps (Poisson distribution) between barostat move proposals.
     */
    public static final String DEFAULT_BAROSTAT_INTERVAL = "10";
    /**
     * Default number of Barostat moves between print statements.
     */
    public static final String DEFAULT_BAROSTAT_PRINT_INTERVAL = "1000";
  
    private static final Logger logger = Logger.getLogger(BarostatOptions.class.getName());
  
    /**
     * The ArgGroup keeps the BarostatOptions together when printing help.
     */
    @ArgGroup(heading = "%n Monte Carlo Pressure Options%n", validate = false)
    private final BarostatOptionGroup group = new BarostatOptionGroup();
  
    /**
     * If pressure has been set > 0, creates a Barostat around a CrystalPotential, else returns the
     * original, unmodified CrystalPotential.
    *
    * @param molecularAssembly Primary molecularAssembly of the CrystalPotential.
    * @param crystalPotential  A CrystalPotential.
    * @return Either a Barostat (NPT enabled) or the CrystalPotential.
    */
   public CrystalPotential checkNPT(MolecularAssembly molecularAssembly,
                                    CrystalPotential crystalPotential) {
     if (group.pressure > 0) {
       return createBarostat(molecularAssembly, crystalPotential);
     } else {
       return crystalPotential;
     }
   }
 
   /**
    * Creates a Barostat around a CrystalPotential.
    *
    * @param assembly         Primary assembly of the CrystalPotential.
    * @param crystalPotential A CrystalPotential.
    * @return An NPT potential.
    * @throws IllegalArgumentException If this BarostatOptions has pressure <= 0.
    */
   public Barostat createBarostat(MolecularAssembly assembly, CrystalPotential crystalPotential)
       throws IllegalArgumentException {
     if (group.pressure > 0) {
       Barostat barostat = new Barostat(assembly, crystalPotential);
       barostat.setPressure(group.pressure);
       barostat.setIsotropic(group.isotropic);
       barostat.setMaxDensity(group.maxD);
       barostat.setMinDensity(group.minD);
       barostat.setBarostatPrintFrequency(group.barPrint);
       double dens = barostat.density();
       if (dens < group.minD) {
         logger.info(format(
             " Barostat: initial density %9.4g < minimum density %9.4g, resetting to minimum density",
             dens, group.minD));
         barostat.setDensity(group.minD);
       } else if (dens > group.maxD) {
         logger.info(format(
             " Barostat: initial density %9.4g > maximum density %9.4g, resetting to maximum density",
             dens, group.maxD));
         barostat.setDensity(group.maxD);
       }
       barostat.setMaxAngleMove(group.maxAM);
       barostat.setMaxVolumeMove(group.maxV);
       barostat.setMeanBarostatInterval(group.barInt);
       return barostat;
     } else {
       throw new IllegalArgumentException(" Pressure is <= 0; cannot create a Barostat!");
     }
   }
 
   /**
    * -p or --npt Specify use of a Monte Carlo Barostat at the given pressure (default 0 = constant
    * volume).
    *
    * @return Returns the pressure (atm).
    */
   public double getPressure() {
     return group.pressure;
   }
 
   public void setPressure(double pressure) {
     group.pressure = pressure;
   }
 
   /**
    * Restrict the MC Barostat to isotropic moves. The lattice angles are * held fixed, and lattice
    * lengths are scaled equally.
    *
    * @return Returns true if the Barostat is isotropic.
    */
   public boolean isIsotropic() {
     return group.isotropic;
   }
 
   public void setIsotropic(boolean isotropic) {
     group.isotropic = isotropic;
   }
 
   /**
    * The maximum density accepted by the MC Barostat (g/cc).
    *
    * @return Returns the maximum density.
    */
   public double getMaxD() {
     return group.maxD;
   }
 
   public void setMaxD(double maxD) {
     group.maxD = maxD;
   }
 
   /**
    * The minimum density accepted by the MC Barostat (g/cc).
    *
    * @return Returns the minimum density.
    */
   public double getMinD() {
     return group.minD;
   }
 
   public void setMinD(double minD) {
     group.minD = minD;
   }
 
   /**
    * The volume of a proposed unit cell volume moves (uniformly distributed) in Angstroms^3.
    *
    * @return Returns the maximum volume move.
    */
   public double getMaxV() {
     return group.maxV;
   }
 
   /**
    * The width of proposed crystal angle moves (uniformly distributed) in degrees.
    *
    * @return Returns the width of angle moves.
    */
   public double getMaxAM() {
     return group.maxAM;
   }
 
   public void setMaxAM(double maxAM) {
     group.maxAM = maxAM;
   }
 
   public void setMaxV(double maxV) {
     group.maxV = maxV;
   }
 
   /**
    * The mean number of MD steps (Poisson distribution) between barostat move proposals.
    *
    * @return Returns the mean number of MD steps between barostat MC trials.
    */
   public int getBarInt() {
     return group.barInt;
   }
 
   public void setBarInt(int barInt) {
     group.barInt = barInt;
   }
 
   /**
    * --bpi or --barostatPrintInterval Sets the number of Barostat MC cycles between print
    * statements.
    */
   public int getPrintInt() {
     return group.barPrint;
   }
 
   public void setPrintInt(int printInterval) {
     group.barPrint = printInterval;
   }
 
   /**
    * Collection of Barostat Options.
    */
   private static class BarostatOptionGroup {
 
     /**
      * -p or --npt Specify use of a Monte Carlo Barostat at the given pressure (default 0 = constant
      * volume).
      */
     @Option(names = {"-p", "--npt"}, paramLabel = "0", defaultValue = "0",
         description = "Specify use of a MC Barostat at the given pressure; the default 0 disables NPT (atm).")
     private double pressure = 0;
     /**
      * -iso or --isotropic Restrict the MC Barostat to isotropic moves. The lattice angles are held
      * fixed, and lattice lengths are scaled equally.
      */
     @Option(names = {"--iso", "--isotropic"},
         defaultValue = "false", description = "Restrict the MC Barostat to isotropic moves.")
     private boolean isotropic = false;
     /**
      * --maxD or --maxDensity Specify the maximum density accepted by the MC Barostat (g/cc).
      */
     @Option(names = {"--maxD", " --maxDensity"},
         paramLabel = DEFAULT_MAX_DENSITY, defaultValue = DEFAULT_MAX_DENSITY,
         description = "Specify the maximum density accepted by the MC Barostat (g/cc).")
     private double maxD = parseDouble(DEFAULT_MAX_DENSITY);
     /**
      * --minD or --minDensity Specify the minimum density accepted by the MC Barostat (g/cc).
      */
     @Option(names = {"--minD", " --minDensity"},
         paramLabel = DEFAULT_MIN_DENSITY, defaultValue = DEFAULT_MIN_DENSITY,
         description = "Specify the minimum density accepted by the MC Barostat (g/cc).")
     private double minD = parseDouble(DEFAULT_MIN_DENSITY);
     @Option(names = {"--maxAM", "--maxAngleMove"},
         paramLabel = DEFAULT_MAX_ANGLE_MOVE, defaultValue = DEFAULT_MAX_ANGLE_MOVE,
         description = "Sets the width of proposed crystal angle moves (uniformly distributed) in degrees.")
     private double maxAM = parseDouble(DEFAULT_MAX_ANGLE_MOVE);
     /**
      * --maxV or --maxVolumeMove Sets the volume move size (uniformly distributed) in Angstroms^3.
      */
     @Option(names = {"--maxV", "--maxVolumeMove"},
         paramLabel = DEFAULT_MAX_VOLUME_MOVE, defaultValue = DEFAULT_MAX_VOLUME_MOVE,
         description = "Default width of proposed unit cell side length moves (uniformly distributed) in Angstroms.")
     private double maxV = parseDouble(DEFAULT_MAX_VOLUME_MOVE);
 
     /**
      * --barInt or --meanBarostatInterval Sets the mean number of MD steps (Poisson distribution)
      * between barostat move proposals.
      */
     @Option(names = {"--barInt", "--meanBarostatInterval"},
         paramLabel = DEFAULT_BAROSTAT_INTERVAL, defaultValue = DEFAULT_BAROSTAT_INTERVAL,
         description = "Sets the mean number of MD steps between barostat move proposals.")
     private int barInt = parseInt(DEFAULT_BAROSTAT_INTERVAL);
     /**
      * --bpi or --barostatPrintInterval Sets the number of Barostat MC cycles between print
      * statements.
      */
     @Option(names = {"--bpi", "--barostatPrintInterval"},
         paramLabel = DEFAULT_BAROSTAT_PRINT_INTERVAL, defaultValue = DEFAULT_BAROSTAT_PRINT_INTERVAL,
         description = "Sets the number of Barostat MC cycles between print statements.")
     private int barPrint = parseInt(DEFAULT_BAROSTAT_PRINT_INTERVAL);
   }
 }