// ******************************************************************************
   //
   // 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
  // and conditions of the license of that module. An independent module is a
  // 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.dynamics.integrators;
  
  import ffx.potential.SystemState;
  import ffx.numerics.Constraint;
  import ffx.numerics.Potential;
  import ffx.potential.ForceFieldEnergy;
  import java.util.ArrayList;
  import java.util.Collection;
  import java.util.List;
  import java.util.logging.Logger;
  import java.util.stream.Collectors;
  
  /**
   * The Integrator class is responsible for propagation of degrees of freedom through time.
   * Implementations must define their behavior at pre-force and post-force evaluation time points.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public abstract class Integrator {
  
    private static final Logger logger = Logger.getLogger(Integrator.class.getName());
    /**
     * Numerical tolerance (as a fraction of bond length) permitted for numerical solutions to
     * constraints.
     */
    protected final double constraintTolerance = ForceFieldEnergy.DEFAULT_CONSTRAINT_TOLERANCE;
  
    /**
     * The MDState class contains the current state of the Molecular Dynamics simulation.
     */
    protected final SystemState state;
    /** Time step (psec). */
    protected double dt;
    /** Any geometric constraints to apply during integration. */
    protected List<Constraint> constraints = new ArrayList<>();
    /** If there are constraints present. */
    protected boolean useConstraints = false;
    /** Half the time step (psec). */
    double dt_2;
  
    /**
     * Constructor for Integrator.
     *
     * @param state The MD state to operate on.
     */
    public Integrator(SystemState state) {
      this.state = state;
      dt = 1.0e-3;
      dt_2 = dt / 2.0;
    }
  
  
    /**
     * Parse an integrator String into an instance of the IntegratorEnum enum.
     *
     * @param str Integrator string.
     * @return Integrator enum.
     */
    public static IntegratorEnum parseIntegrator(String str) {
      try {
        String integrator = str.toUpperCase().replaceAll("\\s+", "");
       integrator = integrator.replaceAll("-", "_");
       return IntegratorEnum.valueOf(integrator);
     } catch (Exception e) {
       logger.info(String.format(" Could not parse %s as an integrator; defaulting to Verlet.", str));
       return IntegratorEnum.VERLET;
     }
   }
 
   /**
    * Adds a set of Constraints that this Integrator must respect.
    *
    * @param addedConstraints Constraints to add.
    */
   public void addConstraints(List<Constraint> addedConstraints) {
     constraints.addAll(addedConstraints);
     useConstraints = true;
   }
 
   /** Copy acceleration to previous acceleration. */
   public void copyAccelerationToPrevious() {
     state.copyAccelerationsToPrevious();
   }
 
   /**
    * Returns a copy of the list of Constraints.
    *
    * @return All Constraints this Integrator respects.
    */
   public List<Constraint> getConstraints() {
     return new ArrayList<>(constraints);
   }
 
   /**
    * Get the time step.
    *
    * @return the time step (psec).
    */
   public double getTimeStep() {
     return dt;
   }
 
   /**
    * Set the time step.
    *
    * @param dt the time step (psec).
    */
   public abstract void setTimeStep(double dt);
 
   /**
    * Integrator post-force evaluation operation.
    *
    * @param gradient the gradient for the post-force operation.
    */
   public abstract void postForce(double[] gradient);
 
   /**
    * Integrator pre-force evaluation operation.
    *
    * @param potential the Potential this integrator operates on.
    */
   public abstract void preForce(Potential potential);
 
 }