// ******************************************************************************
   //
   // 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.
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  // 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
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  // 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
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  package ffx.algorithms.dynamics.thermostats;
  
  import static java.lang.String.format;
  import static org.apache.commons.math3.util.FastMath.sqrt;
  
  import ffx.potential.SystemState;
  import ffx.numerics.Constraint;
  import ffx.numerics.Potential.VARIABLE_TYPE;
  import java.util.Collections;
  import java.util.List;
  
  /**
   * Thermostat a molecular dynamics trajectory to an external bath using the Berendsen weak-coupling
   * thermostat.
   *
   * @author Michael J. Schnieders
   * @see <a href="http://link.aip.org/link/?JCP/81/3684">H. J. C. Berendsen, J. P. M. Postma, W. F.
   *     van Gunsteren, A. DiNola and J. R. Hauk, "Molecular Dynamics with Coupling to an External
   *     Bath", Journal of Chemical Physics, 81, 3684-3690 (1984)</a>
   */
  public class Berendsen extends Thermostat {
  
    /** Berendsen time constant (psec). */
    private double tau;
  
    /**
     * Constructor for Berendsen.
     *
     * @param type The VARIABLE_TYPE of each variable.
     * @param targetTemperature The target temperatures.
     * @param tau Berendsen thermostat time constant (psec).
     */
    public Berendsen(SystemState state, VARIABLE_TYPE[] type, double targetTemperature, double tau) {
      this(state, type, targetTemperature, tau, Collections.emptyList());
    }
  
    public Berendsen(SystemState state, VARIABLE_TYPE[] type, double targetTemperature, double tau,
        List<Constraint> constraints) {
      super(state, type, targetTemperature, constraints);
      this.name = ThermostatEnum.BERENDSEN;
      this.tau = tau;
    }
  
    /**
     * Constructor for Berendsen.
     *
     * @param state The MDState to operate on.
     * @param type The VARIABLE_TYPE of each variable.
     * @param targetTemperature The target temperatures.
     */
    public Berendsen(SystemState state, VARIABLE_TYPE[] type, double targetTemperature) {
      this(state, type, targetTemperature, 0.2e0);
    }
  
    /**
     * {@inheritDoc}
     *
     * <p>Full step velocity modification.
     */
    @Override
    public void fullStep(double dt) {
      double ratio = targetTemperature / state.getTemperature();
     double scale = sqrt(1.0 + (dt / tau) * (ratio - 1.0));
     double[] v = state.v();
     double[] mass = state.getMass();
     for (int i = 0; i < state.getNumberOfVariables(); i++) {
       if (mass[i] > 0.0) {
         v[i] *= scale;
       }
     }
   }
 
   /**
    * Getter for the field <code>tau</code>.
    *
    * @return a double.
    */
   public double getTau() {
     return tau;
   }
 
   /**
    * Setter for the field <code>tau</code>.
    *
    * @param tau a double.
    */
   public void setTau(double tau) {
     this.tau = tau;
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>No velocity modifications are made by the Berendsen method at the half-step.
    */
   @Override
   public void halfStep(double dt) {
   }
 
   /**
    * Add Thermostat details to the kinetic energy and temperature details.
    *
    * @return Description of the thermostat, kinetic energy and temperature.
    */
   public String toThermostatString() {
     return format("\n Berendsen Thermostat (tau = %8.3f psec)\n  %s", tau, super.toString());
   }
 
   /** {@inheritDoc} */
   @Override
   public String toString() {
     return "Berendsen";
   }
 }