Bussi

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//
// Title:       Force Field X.
// Description: Force Field X - Software for Molecular Biophysics.
// Copyright:   Copyright (c) Michael J. Schnieders 2001-2025.
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package ffx.algorithms.dynamics.thermostats;

import ffx.numerics.Constraint;
import ffx.numerics.Potential.VARIABLE_TYPE;
import ffx.potential.SystemState;

import java.util.Collections;
import java.util.List;
import java.util.Random;

import static java.lang.String.format;
import static org.apache.commons.math3.util.FastMath.exp;
import static org.apache.commons.math3.util.FastMath.sqrt;

/**
 * Thermostat a molecular dynamics trajectory to an external bath using the Bussi, Donadio, and
 * Parrinello method. This method is similar to Berendsen thermostat, but generates a canonical
 * distribution.
 *
 * @author Michael J. Schnieders
 * @see <a href="http://dx.doi.org/10.1016/j.cpc.2008.01.006">G. Bussi and M. Parrinello,
 *     "Stochastic Thermostats: Comparison of Local and Global Schemes", Computer Physics
 *     Communications, 179, 26-29 (2008)</a>
 * @since 1.0
 */
public class Bussi extends Thermostat {

  /** The random number generator used to perturb velocities. */
  private final Random bussiRandom;
  /** Bussi thermostat time constant (psec). */
  private double tau;

  /**
   * Constructor for Bussi.
   *
   * @param state The MDState to operate on.
   * @param type the VARIABLE_TYPE of each variable.
   * @param targetTemperature The target temperature.
   * @param tau Bussi thermostat time constant (psec).
   */
  public Bussi(SystemState state, VARIABLE_TYPE[] type, double targetTemperature, double tau) {
    this(state, type, targetTemperature, tau, Collections.emptyList());
  }

  public Bussi(SystemState state, VARIABLE_TYPE[] type, double targetTemperature, double tau,
      List<Constraint> constraints) {
    super(state, type, targetTemperature, constraints);
    this.name = ThermostatEnum.BUSSI;
    this.tau = tau;
    this.bussiRandom = new Random();
  }

  /**
   * Constructor for Bussi.
   *
   * @param state The MDState to operate on.
   * @param type the VARIABLE_TYPE of each variable.
   * @param targetTemperature a double.
   */
  public Bussi(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 expTau = exp(-dt / tau);
    double tempRatio = targetTemperature / state.getTemperature();
    double rate = (1.0 - expTau) * tempRatio / degreesOfFreedom;
    double r = bussiRandom.nextGaussian();
    double s = 0.0;
    for (int i = 0; i < degreesOfFreedom - 1; i++) {
      double si = bussiRandom.nextGaussian();
      s += si * si;
    }
    double scale = expTau + (s + r * r) * rate + 2.0 * r * sqrt(expTau * rate);
    scale = sqrt(scale);
    if (r + sqrt(expTau / rate) < 0.0) {
      scale = -scale;
    }
    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 Bussi method at the half-step.
   */
  @Override
  public void halfStep(double dt) {
  }

  /**
   * {@inheritDoc}
   *
   * <p>Initialize the Random number generator used to apply random forces to the particles.
   */
  public void setRandomSeed(long seed) {
    bussiRandom.setSeed(seed);
  }

  /**
   * 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 Bussi Thermostat (tau = %8.3f psec)\n%s", tau, super.toString());
  }

  /** {@inheritDoc} */
  @Override
  public String toString() {
    return "Bussi";
  }
}