// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2025.
   //
   // 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;
  
  import edu.rit.pj.Comm;
  import ffx.algorithms.AlgorithmListener;
  import ffx.algorithms.Terminatable;
  import ffx.algorithms.dynamics.integrators.BetterBeeman;
  import ffx.algorithms.dynamics.integrators.Integrator;
  import ffx.algorithms.dynamics.integrators.IntegratorEnum;
  import ffx.algorithms.dynamics.integrators.Respa;
  import ffx.algorithms.dynamics.integrators.Stochastic;
  import ffx.algorithms.dynamics.integrators.VelocityVerlet;
  import ffx.algorithms.dynamics.thermostats.Adiabatic;
  import ffx.algorithms.dynamics.thermostats.Berendsen;
  import ffx.algorithms.dynamics.thermostats.Bussi;
  import ffx.algorithms.dynamics.thermostats.Thermostat;
  import ffx.algorithms.dynamics.thermostats.ThermostatEnum;
  import ffx.algorithms.thermodynamics.OrthogonalSpaceTempering;
  import ffx.crystal.Crystal;
  import ffx.numerics.Constraint;
  import ffx.numerics.Potential;
  import ffx.numerics.math.RunningStatistics;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.SystemState;
  import ffx.potential.UnmodifiableState;
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.LambdaInterface;
  import ffx.potential.extended.ExtendedSystem;
  import ffx.potential.openmm.OpenMMEnergy;
  import ffx.potential.parameters.ForceField;
  import ffx.potential.parsers.DYNFilter;
  import ffx.potential.parsers.PDBFilter;
  import ffx.potential.parsers.XPHFilter;
  import ffx.potential.parsers.XYZFilter;
  import ffx.utilities.TinkerUtils;
  import org.apache.commons.configuration2.CompositeConfiguration;
  
  import java.io.File;
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.EnumSet;
  import java.util.List;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  import static ffx.utilities.Constants.FSEC_TO_PSEC;
  import static ffx.utilities.Constants.KCAL_TO_GRAM_ANG2_PER_PS2;
  import static ffx.utilities.Constants.NS2SEC;
  import static ffx.utilities.FileUtils.relativePathTo;
  import static java.lang.String.format;
  import static java.util.Arrays.fill;
  import static org.apache.commons.io.FilenameUtils.getExtension;
  import static org.apache.commons.io.FilenameUtils.removeExtension;
  
  /**
   * Run NVE, NVT, or NPT molecular dynamics.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class MolecularDynamics implements Runnable, Terminatable {
  
    private static final Logger logger = Logger.getLogger(MolecularDynamics.class.getName());
 
   /**
    * The default interval (in picoseconds) between logging the current state.
    */
   private static final double DEFAULT_LOG_INTERVAL = 0.25;
   /**
    * The default interval (in picoseconds) between writing the current state to a DYN file.
    */
   private static final double DEFAULT_RESTART_INTERVAL = 1.0;
   /**
    * The default interval (in picoseconds) between writing the current coordinates.
    */
   private static final double DEFAULT_TRAJECTORY_INTERVAL = 10.0;
   /**
    * By default, wait 25000 nsec (25 usec) in between polling the dynamics thread.
    */
   private static final int DEFAULT_DYNAMICS_SLEEP_TIME = 25000;
 
   /**
    * MolecularAssembly to run dynamics on.
    * <p>
    * For dual or quad topology simulations, this is an array of length 2 or 4.
    */
   protected MolecularAssembly[] molecularAssembly;
   /**
    * Propagate dynamics on this potential surface.
    */
   private final Potential potential;
   /**
    * An Algorithm Listener to send updates to the GUI.
    */
   protected final AlgorithmListener algorithmListener;
   /**
    * Integrator instance.
    */
   private final Integrator integrator;
   /**
    * Thermostat instance.
    */
   private Thermostat thermostat;
   /**
    * Flag to indicate use of constant pressure.
    */
   boolean constantPressure = false;
   /**
    * The Barostat in use, or null if constantPressure is false.
    */
   Barostat barostat = null;
   /**
    * Stores the current molecular dynamics state.
    */
   protected final SystemState state;
   /**
    * State of the system as of the last init call (and start of the last dynamics run).
    */
   protected UnmodifiableState initialState;
   /**
    * A copy of the current MD State. This can be used to revert to a previous state after a rejected
    * MC Move.
    */
   private UnmodifiableState storedState;
 
   /**
    * Temperature Stats for logging.
    */
   private final RunningStatistics temperatureStats = new RunningStatistics();
   /**
    * Potential Energy Stats for logging.
    */
   private final RunningStatistics potentialEnergyStats = new RunningStatistics();
   /**
    * Kinetic Energy Stats for logging.
    */
   private final RunningStatistics kineticEnergyStats = new RunningStatistics();
   /**
    * Total Energy Stats for logging.
    */
   private final RunningStatistics totalEnergyStats = new RunningStatistics();
 
   /**
    * The time step (picoseconds).
    * <p>
    * The method <code>setTimeStep</code> should always be used to set this value.
    */
   protected double dt = 0.001;
   /**
    * The number of MD steps to take.
    */
   private long nSteps = 1000;
   /**
    * Target temperature. ToDo: use the Thermostat instance.
    */
   double targetTemperature = 298.15;
   /**
    * Flag to indicate velocities should be initialized.
    */
   protected boolean initVelocities = true;
   /**
    * Whether MD handles writing restart/trajectory files itself (true), or will be commanded by
    * another class (false) to do it. The latter is true for MC-OST, for example.
    */
   protected boolean automaticWriteouts = true;
   /**
    * The total simulation time.
    */
   protected double totalSimTime = 0.0;
 
   /**
    * Time between writing out restart/checkpoint files in picoseconds.
    */
   protected double restartInterval = DEFAULT_RESTART_INTERVAL;
   /**
    * Time steps between writing out restart/checkpoint files. Set by the init method.
    */
   protected int restartFrequency;
   /**
    * Time between appending to the trajectory file in picoseconds.
    */
   private double trajectoryInterval = DEFAULT_TRAJECTORY_INTERVAL;
   /**
    * Time steps between adding a frame to the trajectory file. Set by the init method.
    */
   protected int trajectoryFrequency;
   /**
    * Time between logging information to the screen in picoseconds.
    */
   private double logInterval = DEFAULT_LOG_INTERVAL;
   /**
    * Time steps between logging information to the screen. Set by the init method.
    */
   protected int logFrequency;
 
   /**
    * File type to use when saving files.
    */
   protected String fileType = "XYZ";
   /**
    * Save snapshots in PDB format.
    */
   boolean saveSnapshotAsPDB = true;
   /**
    * PDB Filter.
    */
   PDBFilter[] pdbFilter = null;
   /**
    * Dynamics restart file.
    */
   File restartFile = null;
   /**
    * Flag to indicate loading of restart file.
    */
   boolean loadRestart = false;
   /**
    * Filter to parse the dynamics restart file.
    */
   DYNFilter dynFilter = null;
   /**
    * If asked to perform dynamics with a null dynamics file, write here.
    */
   private File fallbackDynFile;
 
   /**
    * Log basic information at this level.
    */
   Level basicLogging = Level.INFO;
   /**
    * Indicates how verbose MD should be.
    */
   private MDVerbosity verbosityLevel = MDVerbosity.VERBOSE;
 
   /**
    * Flag to indicate dynamics has been initialized.
    */
   boolean initialized = false;
   /**
    * Flag to indicate MD should be terminated.
    */
   private boolean terminate = false;
   /**
    * Flag to indicate a run has finished.
    */
   protected boolean done;
 
   /**
    * ESV System.
    */
   private ExtendedSystem esvSystem;
   /**
    * ESV Stochastic integrator.
    */
   private Stochastic esvIntegrator;
   /**
    * ESV Adiabatic thermostat.
    */
   private Adiabatic esvThermostat;
   /**
    * Frequency to print ESV info.
    */
   private int printEsvFrequency = -1;
 
   /**
    * If true, the lambda value will be updated each integration time step.
    */
   private boolean nonEquilibriumLambda;
   /**
    * Support for non-equilibrium lambda dynamics.
    */
   private NonEquilbriumDynamics nonEquilibriumDynamics;
 
   /**
    * Constructor for MolecularDynamics.
    *
    * @param assembly            a {@link ffx.potential.MolecularAssembly} object.
    * @param potentialEnergy     a {@link ffx.numerics.Potential} object.
    * @param listener            a {@link ffx.algorithms.AlgorithmListener} object.
    * @param requestedThermostat a {@link ThermostatEnum} object.
    * @param requestedIntegrator a {@link ffx.algorithms.dynamics.integrators.IntegratorEnum}
    *                            object.
    */
   public MolecularDynamics(MolecularAssembly assembly, Potential potentialEnergy,
                            AlgorithmListener listener, ThermostatEnum requestedThermostat,
                            IntegratorEnum requestedIntegrator) {
     this.molecularAssembly = new MolecularAssembly[1];
     this.molecularAssembly[0] = assembly;
     this.algorithmListener = listener;
     this.potential = potentialEnergy;
     if (potentialEnergy instanceof Barostat) {
       constantPressure = true;
       barostat = (Barostat) potentialEnergy;
     }
 
     int numberOfVariables = potentialEnergy.getNumberOfVariables();
     state = new SystemState(numberOfVariables);
     state.setMass(potential.getMass());
 
     CompositeConfiguration properties = molecularAssembly[0].getProperties();
     // If an Integrator wasn't passed to the MD constructor, check for one specified as a property.
     if (requestedIntegrator == null) {
       String integrate = properties.getString("integrate", "VERLET").trim();
       try {
         integrate = integrate.toUpperCase().replace("-", "_");
         requestedIntegrator = IntegratorEnum.valueOf(integrate.toUpperCase());
       } catch (Exception e) {
         requestedIntegrator = IntegratorEnum.VERLET;
       }
     }
 
     boolean oMMLogging = potential instanceof OpenMMEnergy;
     List<Constraint> constraints = potentialEnergy.getConstraints();
 
     // Set the integrator.
     integrator = switch (requestedIntegrator) {
       case RESPA, MTS -> {
         Respa respa = new Respa(state);
         int in = molecularAssembly[0].getProperties().getInt("respa-dt", 4);
         if (in < 2) {
           in = 2;
         }
         if (!oMMLogging) {
           respa.setInnerTimeSteps(in);
         }
         logger.log(Level.FINE, format(" Created a RESPA integrator with %d inner time steps.", in));
         yield respa;
       }
       case STOCHASTIC, LANGEVIN -> {
         double friction = properties.getDouble("friction", 91.0);
         logger.log(Level.FINE, format(" Friction set at %.3f collisions/picosecond", friction));
         Stochastic stochastic = new Stochastic(friction, state);
         if (properties.containsKey("randomseed")) {
           stochastic.setRandomSeed(properties.getInt("randomseed", 0));
         }
         // The stochastic dynamics integration procedure will thermostat
         // the system. The ADIABTIC thermostat just serves to report the
         // temperature and initialize velocities if necessary.
         requestedThermostat = ThermostatEnum.ADIABATIC;
         yield stochastic;
       }
       case BEEMAN -> new BetterBeeman(state);
       default -> new VelocityVerlet(state);
     };
 
     integrator.addConstraints(constraints);
 
     // If a Thermostat wasn't passed to the MD constructor, check for one specified as a property.
     if (requestedThermostat == null) {
       String thermo = properties.getString("thermostat", "Berendsen").trim();
       try {
         thermo = thermo.toUpperCase().replace("-", "_");
         requestedThermostat = ThermostatEnum.valueOf(thermo.toUpperCase());
       } catch (Exception e) {
         requestedThermostat = ThermostatEnum.BERENDSEN;
       }
     }
 
     // Set the thermostat.
     thermostat = switch (requestedThermostat) {
       case BERENDSEN -> {
         double tau = properties.getDouble("tau-temperature", 0.2);
         yield new Berendsen(state, potentialEnergy.getVariableTypes(), targetTemperature, tau,
             constraints);
       }
       case BUSSI -> {
         double tau = properties.getDouble("tau-temperature", 0.2);
         Bussi bussi = new Bussi(state, potentialEnergy.getVariableTypes(), targetTemperature, tau,
             constraints);
         if (properties.containsKey("randomseed")) {
           bussi.setRandomSeed(properties.getInt("randomseed", 0));
         }
         yield bussi;
       }
       default -> new Adiabatic(state, potentialEnergy.getVariableTypes(), constraints);
     };
 
     if (properties.containsKey("randomseed")) {
       thermostat.setRandomSeed(properties.getInt("randomseed", 0));
     }
 
     // For Stochastic dynamics, center of mass motion will not be removed.
     if (integrator instanceof Stochastic) {
       boolean removecom = assembly.getForceField().getBoolean("removecom", false);
       thermostat.setRemoveCenterOfMassMotion(removecom);
       if (removecom) {
         logger.info(" Removing center of mass motion from stochastic simulation.");
       }
     }
 
     done = true;
     fallbackDynFile = defaultFallbackDyn(assembly);
   }
 
   /**
    * Method that determines whether a dynamics is done by the java implementation native to ffx or
    * the OpenMM implementation
    *
    * @param assembly            a {@link ffx.potential.MolecularAssembly} object.
    * @param potentialEnergy     a {@link ffx.numerics.Potential} object.
    * @param listener            a {@link ffx.algorithms.AlgorithmListener} object.
    * @param requestedThermostat a {@link ThermostatEnum} object.
    * @param requestedIntegrator a {@link ffx.algorithms.dynamics.integrators.IntegratorEnum}
    *                            object.
    * @return a {@link MolecularDynamics} object.
    */
   public static MolecularDynamics dynamicsFactory(MolecularAssembly assembly,
                                                   Potential potentialEnergy, AlgorithmListener listener, ThermostatEnum requestedThermostat,
                                                   IntegratorEnum requestedIntegrator) {
 
     return dynamicsFactory(assembly, potentialEnergy, listener, requestedThermostat,
         requestedIntegrator, defaultEngine(assembly, potentialEnergy));
   }
 
   /**
    * dynamicsFactory.
    *
    * @param assembly            a {@link ffx.potential.MolecularAssembly} object.
    * @param potentialEnergy     a {@link ffx.numerics.Potential} object.
    * @param listener            a {@link ffx.algorithms.AlgorithmListener} object.
    * @param requestedThermostat a {@link ThermostatEnum} object.
    * @param requestedIntegrator a {@link ffx.algorithms.dynamics.integrators.IntegratorEnum}
    *                            object.
    * @param engine              a {@link MDEngine} object.
    * @return a {@link MolecularDynamics} object.
    */
   public static MolecularDynamics dynamicsFactory(MolecularAssembly assembly,
                                                   Potential potentialEnergy, AlgorithmListener listener, ThermostatEnum requestedThermostat,
                                                   IntegratorEnum requestedIntegrator, MDEngine engine) {
 
     switch (engine) {
       case OPENMM, OMM -> {
         // TODO: Replace this with calls to the leaves of a proper tree structure.
         // Unfortunately, neither Java, nor Apache Commons, nor Guava has an arbitrary tree
         // implementing Collection.
         // Nor does javax.swing have a quick "get me the leaves" method that I was able to find.
         boolean ommLeaves = potentialEnergy.getUnderlyingPotentials().stream()
             .anyMatch((Potential p) -> p instanceof OpenMMEnergy);
         ommLeaves = ommLeaves || potentialEnergy instanceof OpenMMEnergy;
         if (ommLeaves) {
           return new MolecularDynamicsOpenMM(assembly, potentialEnergy, listener,
               requestedThermostat, requestedIntegrator);
         } else {
           throw new IllegalArgumentException(format(
               " Requested OpenMM engine %s, but at least one leaf of the potential %s is not an OpenMM force field!",
               engine, potentialEnergy));
         }
       }
       default -> {
         return new MolecularDynamics(assembly, potentialEnergy, listener, requestedThermostat,
             requestedIntegrator);
       }
     }
   }
 
   private static MDEngine defaultEngine(MolecularAssembly molecularAssembly,
                                         Potential potentialEnergy) {
     CompositeConfiguration properties = molecularAssembly.getProperties();
     String mdEngine = properties.getString("MD-engine");
     if (mdEngine != null) {
       if (mdEngine.equalsIgnoreCase("OMM")) {
         logger.info(" Creating OpenMM Dynamics Object");
         return MDEngine.OPENMM;
       } else {
         logger.info(" Creating FFX Dynamics Object");
         return MDEngine.FFX;
       }
     } else {
       // TODO: Replace this with a better check.
       boolean ommLeaves = potentialEnergy.getUnderlyingPotentials().stream()
           .anyMatch((Potential p) -> p instanceof OpenMMEnergy);
       ommLeaves = ommLeaves || potentialEnergy instanceof OpenMMEnergy;
       if (ommLeaves) {
         return MDEngine.OPENMM;
       } else {
         return MDEngine.FFX;
       }
     }
   }
 
   /**
    * Creates the "default" fallback dynamics file object (does not create actual file!)
    *
    * @param assembly First assembly.
    * @return Default fallback file.
    */
   private static File defaultFallbackDyn(MolecularAssembly assembly) {
     String firstFileName = removeExtension(assembly.getFile().getAbsolutePath());
     return new File(firstFileName + ".dyn");
   }
 
   /**
    * Adds a MolecularAssembly to be tracked by this MolecularDynamics. Note: does not affect the
    * underlying Potential.
    *
    * @param assembly A MolecularAssembly to be tracked.
    */
   public void addAssembly(MolecularAssembly assembly) {
     molecularAssembly = Arrays.copyOf(molecularAssembly, molecularAssembly.length + 1);
     molecularAssembly[molecularAssembly.length - 1] = assembly;
   }
 
   /**
    * attachExtendedSystem.
    *
    * @param system a {@link ffx.potential.extended.ExtendedSystem} object.
    */
   public void attachExtendedSystem(ExtendedSystem system, double reportFreq) {
     if (esvSystem != null) {
       logger.warning("An ExtendedSystem is already attached to this MD!");
     }
     esvSystem = system;
     SystemState esvState = esvSystem.getState();
     this.esvIntegrator = new Stochastic(esvSystem.getThetaFriction(), esvState);
     if (!esvSystem.getConstraints().isEmpty()) {
       esvIntegrator.addConstraints(esvSystem.getConstraints());
     }
     this.esvThermostat = new Adiabatic(esvState, potential.getVariableTypes());
     printEsvFrequency = intervalToFreq(reportFreq, "Reporting (logging) interval");
     logger.info(
         format("  Attached extended system (%s) to molecular dynamics.", esvSystem.toString()));
     logger.info(format("  Extended System Theta Friction: %f", esvSystem.getThetaFriction()));
     logger.info(format("  Extended System Theta Mass: %f", esvSystem.getThetaMass()));
     logger.info(format("  Extended System Lambda Print Frequency: %d (fsec)", printEsvFrequency));
   }
 
   /**
    * Enables non-equilibrium lambda dynamics.
    *
    * @param nonEquilibrium True if non-equilibrium lambda dynamics should be enabled.
    * @param nEQSteps       Number of lambda steps.
    * @param reverseNEQ     True if lambda path should be reversed.
    */
   public void setNonEquilibriumLambda(boolean nonEquilibrium, int nEQSteps, boolean reverseNEQ) {
     nonEquilibriumLambda = nonEquilibrium;
     if (nonEquilibriumLambda) {
       nonEquilibriumDynamics = new NonEquilbriumDynamics(nEQSteps, reverseNEQ);
     } else {
       nonEquilibriumDynamics = null;
     }
   }
 
   /**
    * Blocking molecular dynamics. When this method returns, the MD run is done.
    *
    * @param nSteps             Number of MD steps
    * @param timeStep           Time step in femtoseconds
    * @param loggingInterval    Interval between printing/logging information in picoseconds.
    * @param trajectoryInterval Interval between adding a frame to the trajectory file in
    *                           picoseconds.
    * @param temperature        Temperature in Kelvins.
    * @param initVelocities     Initialize new velocities from a Maxwell-Boltzmann distribution.
    * @param fileType           XYZ or ARC to save to .arc, PDB for .pdb files
    * @param restartInterval    Interval between writing new restart files in picoseconds.
    * @param dyn                A {@link java.io.File} object to write the restart file to.
    */
   public void dynamic(final long nSteps, final double timeStep, final double loggingInterval,
                       final double trajectoryInterval, final double temperature, final boolean initVelocities,
                       String fileType, double restartInterval, final File dyn) {
     this.fileType = fileType;
     setRestartFrequency(restartInterval);
     dynamic(nSteps, timeStep, loggingInterval, trajectoryInterval, temperature, initVelocities, dyn);
   }
 
   /**
    * Blocking molecular dynamics. When this method returns, the MD run is done.
    *
    * @param nSteps             Number of MD steps
    * @param timeStep           Time step (fsec)
    * @param loggingInterval    Interval between printing/logging information in picoseconds.
    * @param trajectoryInterval Interval between adding a frame to the trajectory file in
    *                           picoseconds.
    * @param temperature        Temperature in Kelvins.
    * @param initVelocities     Initialize new velocities from a Maxwell-Boltzmann distribution.
    * @param dyn                A {@link java.io.File} object to write the restart file to.
    */
   public void dynamic(final long nSteps, final double timeStep, final double loggingInterval,
                       final double trajectoryInterval, final double temperature, final boolean initVelocities,
                       final File dyn) {
     // Return if already running;
     // Could happen if two threads call dynamic on the same MolecularDynamics instance.
     if (!done) {
       logger.warning(" Programming error - a thread invoked dynamic when it was already running.");
       return;
     }
 
     init(nSteps, timeStep, loggingInterval, trajectoryInterval, fileType, restartInterval,
         temperature, initVelocities, dyn);
 
     Thread dynamicThread = new Thread(this);
     dynamicThread.start();
     synchronized (this) {
       try {
         while (dynamicThread.isAlive()) {
           wait(0, DEFAULT_DYNAMICS_SLEEP_TIME);
         }
       } catch (InterruptedException e) {
         String message = " Molecular dynamics interrupted.";
         logger.log(Level.WARNING, message, e);
       }
     }
     if (!verbosityLevel.isQuiet()) {
       logger.info(" Done with an MD round.");
     }
   }
 
   /**
    * Returns the MolecularAssembly array.
    *
    * @return A copy of the MolecularAssembly array.
    */
   public MolecularAssembly[] getAssemblyArray() {
     return molecularAssembly.clone();
   }
 
   /**
    * Returns the associated dynamics file.
    *
    * @return Dynamics restart File.
    */
   public File getDynFile() {
     return restartFile;
   }
 
   /**
    * Gets the kinetic energy at the start of the last dynamics run.
    *
    * @return Kinetic energy at the start of the run.
    */
   public double getInitialKineticEnergy() {
     return initialState.kineticEnergy();
   }
 
   /**
    * Gets the potential energy at the start of the last dynamics run.
    *
    * @return potential energy at the start of the run.
    */
   public double getInitialPotentialEnergy() {
     return initialState.potentialEnergy();
   }
 
   /**
    * Gets the temperature at the start of the last dynamics run.
    *
    * @return temperature at the start of the run.
    */
   public double getInitialTemperature() {
     return initialState.temperature();
   }
 
   /**
    * Gets the total energy at the start of the last dynamics run.
    *
    * @return total energy at the start of the run.
    */
   public double getInitialTotalEnergy() {
     return initialState.getTotalEnergy();
   }
 
   /**
    * getIntervalSteps.
    *
    * @return Always 1 for this implementation.
    */
   public int getIntervalSteps() {
     return 1;
   }
 
   /**
    * No-op; FFX does not need to occasionally return information from FFX.
    *
    * @param intervalSteps Ignored.
    */
   public void setIntervalSteps(int intervalSteps) {
     // Not meaningful for FFX MD.
   }
 
   /**
    * Get the system kinetic energy.
    *
    * @return kinetic energy.
    */
   public double getKineticEnergy() {
     return state.getKineticEnergy();
   }
 
   /**
    * Get the system potential energy.
    *
    * @return potential energy.
    */
   public double getPotentialEnergy() {
     return state.getPotentialEnergy();
   }
 
   /**
    * Get the current temperature of the system
    *
    * @return currentTemperature
    */
   public double getTemperature() {
     return state.getTemperature();
   }
 
   /**
    * Getter for the field <code>thermostat</code>.
    *
    * @return a {@link ffx.algorithms.dynamics.thermostats.Thermostat} object.
    */
   public Thermostat getThermostat() {
     return thermostat;
   }
 
   /**
    * Setter for the field <code>thermostat</code>.
    *
    * @param thermostat a {@link ffx.algorithms.dynamics.thermostats.Thermostat} object.
    */
   public void setThermostat(Thermostat thermostat) {
     this.thermostat = thermostat;
   }
 
   /**
    * getTimeStep.
    *
    * @return Time step in picoseconds.
    */
   public double getTimeStep() {
     return dt;
   }
 
   /**
    * Sets the time step and resets frequencies based on stored intervals.
    *
    * @param step Time step in femtoseconds.
    */
   private void setTimeStep(double step) {
     dt = step * FSEC_TO_PSEC;
     // Reset frequencies to be consistent with new time step.
     setRestartFrequency(restartInterval);
     setLoggingFrequency(logInterval);
     setTrajectoryFrequency(trajectoryInterval);
   }
 
   /**
    * Get the total system energy (kinetic plus potential).
    *
    * @return total energy.
    */
   public double getTotalEnergy() {
     return state.getTotalEnergy();
   }
 
   public MDVerbosity getVerbosityLevel() {
     return verbosityLevel;
   }
 
   public void setVerbosityLevel(MDVerbosity level) {
     verbosityLevel = level;
     if (level == MDVerbosity.SILENT) {
       basicLogging = Level.FINE;
     } else {
       basicLogging = Level.INFO;
     }
   }
 
   /**
    * init
    *
    * @param nSteps             Number of MD steps
    * @param timeStep           Time step in femtoseconds
    * @param loggingInterval    Interval between printing/logging information in picoseconds.
    * @param trajectoryInterval Interval between adding a frame to the trajectory file in
    *                           picoseconds.
    * @param fileType           XYZ or ARC to save to .arc, PDB for .pdb files
    * @param restartInterval    Interval between writing new restart files in picoseconds.
    * @param temperature        Temperature in Kelvins.
    * @param initVelocities     Initialize new velocities from a Maxwell-Boltzmann distribution.
    * @param dyn                A {@link java.io.File} object to write the restart file to.
    */
   public void init(final long nSteps, final double timeStep, final double loggingInterval,
                    final double trajectoryInterval, final String fileType, final double restartInterval,
                    final double temperature, final boolean initVelocities, final File dyn) {
 
     // Return if already running.
     if (!done) {
       logger.warning(
           " Programming error - attempt to modify parameters of a running MolecularDynamics instance.");
       return;
     }
 
     if (integrator instanceof Stochastic) {
       if (constantPressure) {
         logger.log(basicLogging, "\n Stochastic dynamics in the NPT ensemble");
       } else {
         logger.log(basicLogging, "\n Stochastic dynamics in the NVT ensemble");
       }
     } else if (!(thermostat instanceof Adiabatic)) {
       if (constantPressure) {
         logger.log(basicLogging, "\n Molecular dynamics in the NPT ensemble");
       } else {
         logger.log(basicLogging, "\n Molecular dynamics in the NVT ensemble");
       }
     } else {
       if (constantPressure) {
         logger.severe("\n NPT Molecular dynamics requires a thermostat");
       } else {
         logger.log(basicLogging, "\n Molecular dynamics in the NVE ensemble");
       }
     }
 
     this.nSteps = nSteps;
     totalSimTime = 0.0;
 
     // Convert the time step from femtoseconds to picoseconds.
     setTimeStep(timeStep);
 
     // Convert intervals in ps to frequencies in time steps.
     setLoggingFrequency(loggingInterval);
     setTrajectoryFrequency(trajectoryInterval);
     setRestartFrequency(restartInterval);
 
     checkFrequency("Reporting           ", logFrequency);
     if (automaticWriteouts) {
       // Only sanity check these values if MD is doing this itself.
       checkFrequency("Trajectory Write-Out", trajectoryFrequency);
       checkFrequency("Restart             ", restartFrequency);
     }
 
     // Set snapshot file type.
     saveSnapshotAsPDB = true;
     if (fileType.equalsIgnoreCase("XYZ") || fileType.equalsIgnoreCase("ARC")) {
       saveSnapshotAsPDB = false;
     } else if (!fileType.equalsIgnoreCase("PDB")) {
       logger.warning("Snapshot file type unrecognized; saving snapshots as PDB.\n");
     }
 
     setArchiveFile();
 
     this.restartFile = (dyn == null) ? fallbackDynFile : dyn;
     loadRestart = restartFile.exists() && !initialized;
 
     if (dynFilter == null) {
       dynFilter = new DYNFilter(molecularAssembly[0].getName());
     }
 
     this.targetTemperature = temperature;
     this.initVelocities = initVelocities;
     done = false;
 
     if (loadRestart) {
       logger.info("  Continuing from " + restartFile.getAbsolutePath());
     }
 
     if (!verbosityLevel.isQuiet()) {
       logger.info(format("  Integrator:          %15s", integrator.toString()));
       logger.info(format("  Thermostat:          %15s", thermostat.toString()));
       logger.info(format("  Number of steps:     %8d", nSteps));
       logger.info(format("  Time step:           %8.3f (fsec)", timeStep));
       logger.info(format("  Print interval:      %8.3f (psec)", loggingInterval));
       logger.info(format("  Save interval:       %8.3f (psec)", trajectoryInterval));
       if (molecularAssembly.length > 1) {
         for (int i = 0; i < molecularAssembly.length; i++) {
           File archiveFile = molecularAssembly[i].getArchiveFile();
           logger.info(format("  Archive file %3d: %s", (i + 1), archiveFile.getAbsolutePath()));
         }
       } else {
         logger.info(format("  Archive file:     %s",
             molecularAssembly[0].getArchiveFile().getAbsolutePath()));
       }
       logger.info(format("  Restart file:     %s", restartFile.getAbsolutePath()));
     }
   }
 
   /**
    * A version of init with the original method header. Redirects to the new method with default
    * values for added parameters. Needed by (at least) ReplicaExchange, which calls this directly.
    *
    * @param nSteps             Number of MD steps
    * @param timeStep           Time step in femtoseconds
    * @param loggingInterval    Interval between printing/logging information in picoseconds.
    * @param trajectoryInterval Interval between adding a frame to the trajectory file in
    *                           picoseconds.
    * @param temperature        Temperature in Kelvins.
    * @param initVelocities     Initialize new velocities from a Maxwell-Boltzmann distribution.
    * @param dyn                A {@link java.io.File} object to write the restart file to.
    */
   public void init(final long nSteps, final double timeStep, final double loggingInterval,
                    final double trajectoryInterval, final double temperature, final boolean initVelocities,
                    final File dyn) {
     init(nSteps, timeStep, loggingInterval, trajectoryInterval, "XYZ", restartInterval, temperature,
         initVelocities, dyn);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void run() {
     try {
       preRunOps();
     } catch (IllegalStateException ise) {
       return;
     }
     initializeEnergies();
     postInitEnergies();
     mainLoop();
     postRun();
   }
 
   /**
    * Enable or disable automatic writeout of trajectory snapshots and restart files.
    *
    * <p>Primarily intended for use with MC-OST, which handles the timing itself.
    *
    * @param autoWriteout Whether to automatically write out trajectory and restart files.
    */
   public void setAutomaticWriteouts(boolean autoWriteout) {
     this.automaticWriteouts = autoWriteout;
   }
 
   /**
    * Sets the "fallback" .dyn file to write to if none is passed to the dynamic method.
    *
    * @param fallback Fallback dynamics restart file.
    */
   public void setFallbackDynFile(File fallback) {
     this.fallbackDynFile = fallback;
   }
 
   /**
    * Method to set file type from groovy scripts.
    *
    * @param fileType the type of snapshot files to write.
    */
   public void setFileType(String fileType) {
     this.fileType = fileType;
   }
 
   /**
    * Not meaningful for FFX dynamics (no need to obtain velocities/accelerations from a different
    * program, especially one running on a GPU). Is a no-op.
    *
    * @param obtainVA Not meaningful for this implementation.
    */
   public void setObtainVelAcc(boolean obtainVA) {
     // Not meaningful for FFX dynamics.
   }
 
   /**
    * Method to set the Restart Frequency.
    *
    * @param restartInterval Time in ps between writing restart files.
    * @throws java.lang.IllegalArgumentException If restart frequency is not a positive number
    */
   public void setRestartFrequency(double restartInterval) throws IllegalArgumentException {
     restartFrequency = intervalToFreq(restartInterval, "Restart interval");
     this.restartInterval = restartInterval;
   }
 
   /**
    * Set the archive file for each MolecularAssembly.
    *
    * @param archiveFiles An array of archive files.
    */
   public void setArchiveFiles(File[] archiveFiles) {
     logger.info(" Setting archive files:\n " + Arrays.toString(archiveFiles));
     int n = molecularAssembly.length;
     assert archiveFiles.length == n;
     for (int i = 0; i < n; i++) {
       molecularAssembly[i].setArchiveFile(archiveFiles[i]);
     }
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void terminate() {
     terminate = true;
     while (!done) {
       synchronized (this) {
         try {
           wait(1);
         } catch (Exception e) {
           logger.log(Level.WARNING, " Exception terminating dynamics.\n", e);
         }
       }
     }
   }
 
   /**
    * Write restart and trajectory files if the provided step matches the frequency and that file type
    * is requested.
    *
    * @param step        Step to write files (if any) for.
    * @param trySnapshot If false, do not write snapshot even if the time step is correct.
    * @param tryRestart  If false, do not write a restart file even if the time step is correct.
    * @return EnumSet of actions taken by this method.
    */
   public EnumSet<MDWriteAction> writeFilesForStep(long step, boolean trySnapshot,
                                                   boolean tryRestart) {
     return writeFilesForStep(step, trySnapshot, tryRestart, null);
   }
 
   /**
    * Write restart and trajectory files if the provided step matches the frequency and that file type
    * is requested.
    *
    * @param step        Step to write files (if any) for.
    * @param trySnapshot If false, do not write snapshot even if the time step is correct.
    * @param tryRestart  If false, do not write a restart file even if the time step is correct.
    * @param extraLines  Additional lines to append into the comments section of the snapshot (or
    *                    null).
    * @return EnumSet of actions taken by this method.
    */
   public EnumSet<MDWriteAction> writeFilesForStep(long step, boolean trySnapshot, boolean tryRestart,
                                                   String[] extraLines) {
     List<String> linesList =
         (extraLines == null) ? new ArrayList<>() : new ArrayList<>(Arrays.asList(extraLines));
 
     if (potential instanceof LambdaInterface) {
       String lamString = format("Lambda: %.8f", ((LambdaInterface) potential).getLambda());
       linesList.add(lamString);
     }
 
     String tempString = format("Temp: %.2f", thermostat.getTargetTemperature());
     linesList.add(tempString);
 
     String timeString = format(" Time: %7.3e", totalSimTime);
     linesList.add(timeString);
 
     if (esvSystem != null) {
       String pHString = format("pH: %.2f", esvSystem.getConstantPh());
       linesList.add(pHString);
     }
 
     Comm world = Comm.world();
     if (world != null && world.size() > 1) {
       String rankString = format("Rank: %d", world.rank());
       linesList.add(rankString);
     }
 
     String[] allLines = new String[linesList.size()];
     allLines = linesList.toArray(allLines);
 
     EnumSet<MDWriteAction> written = EnumSet.noneOf(MDWriteAction.class);
     if (step != 0) {
       // Write out snapshots in selected format every saveSnapshotFrequency steps.
       if (trySnapshot && trajectoryFrequency > 0 && step % trajectoryFrequency == 0) {
 
         // Log stats.
         logger.info(format("\n Average Values for the Last %d Out of %d Dynamics Steps\n",
             trajectoryFrequency, step));
         logger.info(format("  Simulation Time  %16.4f Picosecond", step * dt));
         logger.info(format("  Total Energy     %16.4f Kcal/mole   (+/-%9.4f)", totalEnergyStats.getMean(),
             totalEnergyStats.getStandardDeviation()));
         logger.info(format("  Potential Energy %16.4f Kcal/mole   (+/-%9.4f)",
             potentialEnergyStats.getMean(), potentialEnergyStats.getStandardDeviation()));
         logger.info(format("  Kinetic Energy   %16.4f Kcal/mole   (+/-%9.4f)", kineticEnergyStats.getMean(),
             kineticEnergyStats.getStandardDeviation()));
         logger.info(format("  Temperature      %16.4f Kelvin      (+/-%9.4f)\n", temperatureStats.getMean(),
             temperatureStats.getStandardDeviation()));
         totalEnergyStats.reset();
         potentialEnergyStats.reset();
         kineticEnergyStats.reset();
         temperatureStats.reset();
 
         if (esvSystem != null) {
           for (Atom atom : molecularAssembly[0].getAtomList()) {
             int atomIndex = atom.getIndex() - 1;
             atom.setOccupancy(esvSystem.getTitrationLambda(atomIndex));
             atom.setTempFactor(esvSystem.getTautomerLambda(atomIndex));
           }
         }
         appendSnapshot(allLines);
         written.add(MDWriteAction.SNAPSHOT);
       }
 
       // Write out restart files every saveRestartFileFrequency steps.
       if (tryRestart && restartFrequency > 0 && step % restartFrequency == 0) {
         writeRestart();
         written.add(MDWriteAction.RESTART);
       }
     }
     return written;
   }
 
   /**
    * Write out a restart file.
    */
   public void writeRestart() {
     String dynName = relativePathTo(restartFile).toString();
     double[] x = state.x();
     double[] v = state.v();
     double[] a = state.a();
     double[] aPrevious = state.aPrevious();
     if (dynFilter.writeDYN(restartFile, molecularAssembly[0].getCrystal(), x, v, a, aPrevious)) {
       logger.log(basicLogging, format(" Wrote dynamics restart to:  %s.", dynName));
     } else {
       logger.log(basicLogging, format(" Writing dynamics restart failed:  %s.", dynName));
     }
     if (esvSystem != null) {
       esvSystem.writeRestart();
       esvSystem.writeLambdaHistogram(false);
     }
     potential.writeAdditionalRestartInfo(true);
   }
 
   /**
    * Set the archive file for each MolecularAssembly (if not already set).
    */
   private void setArchiveFile() {
     for (MolecularAssembly assembly : molecularAssembly) {
       File file = assembly.getFile();
       String filename = removeExtension(file.getAbsolutePath());
       File archiveFile = assembly.getArchiveFile();
       if (archiveFile == null) {
         archiveFile = new File(filename + ".arc");
         assembly.setArchiveFile(XYZFilter.version(archiveFile));
       }
     }
   }
 
   /**
    * Converts an interval in ps to a frequency in time steps.
    *
    * @param interval Interval between events in ps
    * @param describe Description of the event.
    * @return Frequency of event in time steps per event.
    * @throws IllegalArgumentException If interval is not a positive finite value.
    */
   private int intervalToFreq(double interval, String describe) throws IllegalArgumentException {
     if (!Double.isFinite(interval) || interval <= 0) {
       throw new IllegalArgumentException(
           format(" %s must be " + "positive finite value in ps, was %10.4g", describe, interval));
     }
     if (interval >= dt) {
       return (int) (interval / dt);
     } else {
       logger.warning(format(" Specified %s of %.6f ps < time step %.6f ps; "
           + "interval is set to once per time step!", describe, interval, dt));
       return 1;
     }
   }
 
   /**
    * Method to set the logging/printing frequency.
    *
    * @param logInterval Time in ps between logging information to the screen.
    */
   private void setLoggingFrequency(double logInterval) {
     logFrequency = intervalToFreq(logInterval, "Reporting (logging) interval");
     this.logInterval = logInterval;
   }
 
   /**
    * Method to set the frequency of appending snapshots to the trajectory file.
    *
    * @param snapshotInterval Time in ps between appending snapshots to the trajectory file.
    */
   private void setTrajectoryFrequency(double snapshotInterval) {
     trajectoryFrequency = intervalToFreq(snapshotInterval, "Trajectory writeout interval");
     this.trajectoryInterval = snapshotInterval;
   }
 
   /**
    * Performs basic pre-MD operations such as loading the restart file.
    */
   void preRunOps() throws IllegalStateException {
     done = false;
     terminate = false;
 
     // Set the target temperature.
     thermostat.setTargetTemperature(targetTemperature);
     boolean quiet = verbosityLevel.isQuiet();
     thermostat.setQuiet(quiet);
     if (integrator instanceof Stochastic stochastic) {
       stochastic.setTemperature(targetTemperature);
     }
 
     // Set the step size.
     integrator.setTimeStep(dt);
 
     if (!initialized) {
       // Initialize from a restart file.
       if (loadRestart) {
         Crystal crystal = molecularAssembly[0].getCrystal();
         double[] x = state.x();
         double[] v = state.v();
         double[] a = state.a();
         double[] aPrevious = state.aPrevious();
         if (!dynFilter.readDYN(restartFile, crystal, x, v, a, aPrevious)) {
           String message = " Could not load the restart file - dynamics terminated.";
           logger.log(Level.WARNING, message);
           done = true;
           throw new IllegalStateException(message);
         } else {
           molecularAssembly[0].setCrystal(crystal);
         }
       } else {
         // Initialize using current atomic coordinates.
         potential.getCoordinates(state.x());
         // Initialize atomic velocities from a Maxwell-Boltzmann distribution or set to 0.
         if (initVelocities) {
           thermostat.maxwell(targetTemperature);
         } else {
           fill(state.v(), 0.0);
         }
       }
     } else {
       // If MD has already been run (i.e., Annealing or RepEx), then initialize velocities if
       // requested.
       if (initVelocities) {
         thermostat.maxwell(targetTemperature);
       }
     }
   }
 
   /**
    * Initializes energy fields, esp. potential energy.
    */
   private void initializeEnergies() {
     // Compute the current potential energy.
     double[] x = state.x();
     double[] gradient = state.gradient();
 
     boolean propagateLambda = true;
     if (potential instanceof OrthogonalSpaceTempering orthogonalSpaceTempering) {
       propagateLambda = orthogonalSpaceTempering.getPropagateLambda();
       orthogonalSpaceTempering.setPropagateLambda(false);
     }
 
     if (esvSystem != null && potential instanceof OpenMMEnergy) {
       state.setPotentialEnergy(((OpenMMEnergy) potential).energyAndGradientFFX(x, gradient));
     } else {
       state.setPotentialEnergy(potential.energyAndGradient(x, gradient));
     }
 
     if (potential instanceof OrthogonalSpaceTempering orthogonalSpaceTempering) {
       orthogonalSpaceTempering.setPropagateLambda(propagateLambda);
     }
 
     // Initialize current and previous accelerations.
     if (!loadRestart || initialized || integrator instanceof Respa) {
       // For the Respa integrator, initial accelerations are from the slowly varying forces.
       if (integrator instanceof Respa) {
         potential.setEnergyTermState(Potential.STATE.SLOW);
         potential.energyAndGradient(x, gradient);
       }
 
       int numberOfVariables = state.getNumberOfVariables();
       double[] a = state.a();
       double[] mass = state.getMass();
       for (int i = 0; i < numberOfVariables; i++) {
         a[i] = -KCAL_TO_GRAM_ANG2_PER_PS2 * gradient[i] / mass[i];
       }
       state.copyAccelerationsToPrevious();
     }
 
     if (esvSystem != null) {
       SystemState esvState = esvSystem.getState();
       double[] esvA = esvState.a();
       double[] esvMass = esvState.getMass();
       int nESVs = esvState.getNumberOfVariables();
       double[] gradESV = esvSystem.postForce();
       for (int i = 0; i < nESVs; i++) {
         esvA[i] = -KCAL_TO_GRAM_ANG2_PER_PS2 * gradESV[i] / esvMass[i];
       }
     }
 
     // Compute the current kinetic energy.
     thermostat.computeKineticEnergy();
     if (esvSystem != null) {
       esvThermostat.computeKineticEnergy();
       double kineticEnergy = thermostat.getKineticEnergy();
       double esvKineticEnergy = esvThermostat.getKineticEnergy();
       state.setKineticEnergy(kineticEnergy + esvKineticEnergy);
     }
 
     // Store the initial state.
     initialState = new UnmodifiableState(state);
 
     // Reset the statistics.
     temperatureStats.reset();
     potentialEnergyStats.reset();
     kineticEnergyStats.reset();
     totalEnergyStats.reset();
   }
 
   /**
    * Pre-run operations (mostly logging) that require knowledge of system energy.
    */
   void postInitEnergies() {
     initialized = true;
 
     logger.log(basicLogging,
         format("\n  %8s %12s %12s %12s %8s %8s", "Time", "Kinetic", "Potential", "Total", "Temp", "CPU"));
     logger.log(basicLogging,
         format("  %8s %12s %12s %12s %8s %8s", "psec", "kcal/mol", "kcal/mol", "kcal/mol", "K", "sec"));
     logger.log(basicLogging, format("  %8s %12.4f %12.4f %12.4f %8.2f", "", state.getKineticEnergy(),
         state.getPotentialEnergy(), state.getTotalEnergy(), state.getTemperature()));
 
     // Store the initialized state.
     storeState();
   }
 
   /**
    * Post-run cleanup operations.
    */
   void postRun() {
     // Add the potential energy of the slow degrees of freedom.
     if (integrator instanceof Respa) {
       potential.setEnergyTermState(Potential.STATE.BOTH);
     }
 
     // Log normal completion.
     if (!terminate) {
       logger.log(basicLogging, format(" Completed %8d time steps\n", nSteps));
     }
 
     // Reset the done and terminate flags.
     done = true;
     terminate = false;
   }
 
   /**
    * Append a snapshot to the trajectory file.
    *
    * @param extraLines Strings of meta-data to include.
    */
   protected void appendSnapshot(String[] extraLines) {
     int numAssemblies = molecularAssembly.length;
     int currentAssembly = 0;
     // Loop over all molecular assemblies.
     for (MolecularAssembly assembly : molecularAssembly) {
       File archiveFile = assembly.getArchiveFile();
       ForceField forceField = assembly.getForceField();
       CompositeConfiguration properties = assembly.getProperties();
 
       //Remove energy/density from name of assembly as it likely changed during MD.
       String name = assembly.getName();
       String[] tokens = name.split(" +");
       StringBuilder stringBuilder = new StringBuilder();
       int numTokens = tokens.length;
       for (int i = 0; i < numTokens; i++) {
         if (tokens[i].equalsIgnoreCase("Energy:") || tokens[i].equalsIgnoreCase("Density:")) {
           //Skip next value.
           i++;
         } else {
           stringBuilder.append(" ").append(tokens[i]);
         }
       }
       assembly.setName(stringBuilder.toString());
 
       // Save as an ARC file.
       if (archiveFile != null && !saveSnapshotAsPDB) {
         String aiName = relativePathTo(archiveFile).toString();
         if (esvSystem == null) {
           XYZFilter xyzFilter = new XYZFilter(archiveFile, assembly, forceField, properties);
           if (xyzFilter.writeFile(archiveFile, true, extraLines)) {
             logger.log(basicLogging, format(" Appended snapshot to:       %s", aiName));
           } else {
             logger.warning(format(" Appending snapshot failed:  %s", aiName));
           }
         } else {
           XPHFilter xphFilter = new XPHFilter(archiveFile, assembly, forceField, properties, esvSystem);
           if (xphFilter.writeFile(archiveFile, true, extraLines)) {
             logger.log(basicLogging, format(" Appended to XPH archive %s", aiName));
           } else {
             logger.warning(format(" Appending to XPH archive %s failed.", aiName));
           }
         }
       } else if (saveSnapshotAsPDB) {
         if (pdbFilter == null) {
           pdbFilter = new PDBFilter[numAssemblies];
         }
         if (pdbFilter[currentAssembly] == null) {
           File file = assembly.getFile();
           String extName = getExtension(file.getName());
           File pdbFile;
           if (extName.toLowerCase().startsWith("pdb")) {
             // Version the file to avoid appending to the original input file.
             pdbFile = TinkerUtils.version(file);
           } else {
             String filename = removeExtension(file.getAbsolutePath());
             pdbFile = new File(filename + ".pdb");
           }
           pdbFilter[currentAssembly] = new PDBFilter(pdbFile, assembly, forceField, properties);
           pdbFilter[currentAssembly].setModelNumbering(0);
         }
         File pdbFile = pdbFilter[currentAssembly].getFile();
         String aiName = relativePathTo(pdbFile).toString();
         if (pdbFilter[currentAssembly].writeFile(pdbFile, true, extraLines)) {
           logger.log(basicLogging, format(" Appended to PDB file %s", aiName));
         } else {
           logger.warning(format(" Appending to PDB file to %s failed.", aiName));
         }
       }
       currentAssembly++;
     }
   }
 
   /**
    * Checks if thermodynamics must be logged. If logged, current time is returned, else the time
    * passed in is returned.
    *
    * @param step Time step to possibly log thermodynamics for.
    * @param time Clock time (in nsec) thermodynamics was last logged.
    * @return Either current time (if logged), else the time variable passed in.
    */
   protected long logThermoForTime(long step, long time) {
     if (step % logFrequency == 0) {
       return logThermodynamics(time);
     } else {
       return time;
     }
   }
 
   /**
    * Log thermodynamics to the screen.
    *
    * @param time Clock time (in nsec) since this was last called.
    * @return Clock time at the end of this call.
    */
   private long logThermodynamics(long time) {
     time = System.nanoTime() - time;
     logger.log(basicLogging,
         format(" %7.3e %12.4f %12.4f %12.4f %8.2f %8.3f", totalSimTime, state.getKineticEnergy(),
             state.getPotentialEnergy(), state.getTotalEnergy(), state.getTemperature(),
             time * NS2SEC));
     return System.nanoTime();
   }
 
   /**
    * Main loop of the run method.
    */
   private void mainLoop() {
     // Integrate Newton's equations of motion for the requested number of steps,
     // unless early termination is requested.
     long time = System.nanoTime();
     int removeCOMMotionFrequency = molecularAssembly[0].getForceField().getInteger("removecomfrequency", 100);
     if (thermostat.getRemoveCenterOfMassMotion()) {
       logger.info(format(" COM will be removed every %3d step(s).", removeCOMMotionFrequency));
     }
 
     if (nonEquilibriumLambda) {
       // Configure the number of non-equilibrium dynamics.
       nSteps = nonEquilibriumDynamics.setMDSteps(nSteps);
       LambdaInterface lambdaInterface = (LambdaInterface) potential;
       double lambda = nonEquilibriumDynamics.getInitialLambda();
       lambdaInterface.setLambda(lambda);
     }
 
     // Main MD loop to take molecular dynamics steps.
     for (long step = 1; step <= nSteps; step++) {
 
       // Update lambda for non-equilibrium simulations.
       if (nonEquilibriumLambda && nonEquilibriumDynamics.isUpdateStep(step)) {
         Potential.STATE respaState = potential.getEnergyTermState();
         if (integrator instanceof Respa) {
           if (respaState != Potential.STATE.BOTH) {
             potential.setEnergyTermState(Potential.STATE.BOTH);
           }
         }
         LambdaInterface lambdaInterface = (LambdaInterface) potential;
         double currentLambda = lambdaInterface.getLambda();
         double currentEnergy = state.getPotentialEnergy();
         // Update the lambda value.
         double newLambda = nonEquilibriumDynamics.getNextLambda(step, currentLambda);
         lambdaInterface.setLambda(newLambda);
         // Compute the new energy.
         double newEnergy = potential.energy(state.x());
         // The non-equilibrium work is the difference in energy.
         double dW = newEnergy - currentEnergy;
         nonEquilibriumDynamics.addWork(dW);
         logger.info(format(" Non-equilibrium L=%5.3f Work=%12.6f", newLambda, nonEquilibriumDynamics.getWork()));
 
         // Reset the Respa State.
         if (integrator instanceof Respa) {
           potential.setEnergyTermState(respaState);
         }
       }
 
       if (step > 1) {
         List<Constraint> constraints = potential.getConstraints();
         // TODO: Replace magic numbers with named constants.
         long constraintFails = constraints.stream()
             .filter((Constraint c) -> !c.constraintSatisfied(state.x(), state.v(), 1E-7, 1E-7)).count();
         if (constraintFails > 0) {
           logger.info(format(" %d constraint failures in step %d", constraintFails, step));
         }
       }
 
       // Do the half-step thermostat operation.
       thermostat.halfStep(dt);
 
       // Do the half-step integration operation.
       integrator.preForce(potential);
       if (esvSystem != null) {
         esvIntegrator.preForce(potential);
         //preForce processes theta values after
         esvSystem.preForce();
       }
 
       // Compute the potential energy and gradients.
       if (esvSystem != null && potential instanceof OpenMMEnergy) {
         state.setPotentialEnergy(((OpenMMEnergy) potential).energyAndGradientFFX(state.x(), state.gradient()));
       } else {
         state.setPotentialEnergy(potential.energyAndGradient(state.x(), state.gradient()));
       }
 
       // Add the potential energy of the slow degrees of freedom.
       if (integrator instanceof Respa r) {
         double potentialEnergy = state.getPotentialEnergy();
         state.setPotentialEnergy(potentialEnergy + r.getHalfStepEnergy());
       }
 
       // Do the full-step integration operation.
       integrator.postForce(state.gradient());
       if (esvSystem != null) {
         double[] dEdL = esvSystem.postForce();
         esvIntegrator.postForce(dEdL);
       }
 
       // Compute the full-step kinetic energy.
       thermostat.computeKineticEnergy();
 
       // Do the full-step thermostat operation.
       thermostat.fullStep(dt);
 
       // Recompute the kinetic energy after the full-step thermostat operation.
       thermostat.computeKineticEnergy();
       if (esvSystem != null) {
         // Adiabatic thermostat does nothing at half step.
         esvThermostat.computeKineticEnergy();
       }
 
       // Remove center of mass motion if requested.
       if (thermostat.getRemoveCenterOfMassMotion() && step % removeCOMMotionFrequency == 0) {
         thermostat.centerOfMassMotion(true, false);
       }
 
       // Collect current kinetic energy, temperature, and total energy.
       if (esvSystem != null) {
         double kineticEnergy = thermostat.getKineticEnergy();
         double esvKineticEnergy = esvThermostat.getKineticEnergy();
         state.setKineticEnergy(kineticEnergy + esvKineticEnergy);
       }
 
       // Collect running statistics.
       temperatureStats.addValue(state.getTemperature());
       potentialEnergyStats.addValue(state.getPotentialEnergy());
       kineticEnergyStats.addValue(state.getKineticEnergy());
       totalEnergyStats.addValue(state.getTotalEnergy());
 
       // Update atomic velocity, acceleration and previous acceleration.
       potential.setVelocity(state.v());
       potential.setAcceleration(state.a());
       potential.setPreviousAcceleration(state.aPrevious());
 
       // Log the current state every printFrequency steps.
       totalSimTime += dt;
       time = logThermoForTime(step, time);
       if (step % printEsvFrequency == 0 && esvSystem != null) {
         logger.log(basicLogging, format(" %s", esvSystem.getLambdaList()));
       }
 
       if (automaticWriteouts) {
         writeFilesForStep(step, true, true);
       }
 
       // Notify the algorithmListeners.
       if (algorithmListener != null && step % logFrequency == 0) {
         for (MolecularAssembly assembly : molecularAssembly) {
           algorithmListener.algorithmUpdate(assembly);
         }
       }
 
       // Check for a termination request.
       if (terminate) {
         logger.info(format("\n Terminating after %8d time steps\n", step));
         break;
       }
     }
   }
 
   /**
    * Perform a sanity check on a frequency to ensure it's not longer than total runtime. Currently,
    * the setter parameter is ignored due to issues with our test suite.
    *
    * @param describe  Description of the frequency.
    * @param frequency Frequency in time steps.
    */
   private void checkFrequency(String describe, int frequency) {
     if (frequency > nSteps) {
       logger.fine(
           format(" Specified %s frequency of %d is greater than the number of steps %d", describe,
               frequency, nSteps));
     }
   }
 
   /**
    * Set the coordinates.
    *
    * @param coords The coordinates to copy into MD coordinates array.
    */
   public void setCoordinates(double[] coords) {
     state.setCoordinates(coords);
   }
 
   /**
    * Get the coordinates.
    *
    * @return A copy of the current coordinates are returned.
    */
   public double[] getCoordinates() {
     return state.getCoordinatesCopy();
   }
 
   /**
    * Store the current state of the molecular dynamics simulation in a MDState record.
    */
   public void storeState() {
     storedState = state.getUnmodifiableState();
   }
 
   /**
    * Revert the state of the MolecularDynamics instance to the stored MDState.
    *
    * @throws Exception is thrown if the stored state is null.
    */
   public void revertState() throws Exception {
     if (storedState == null) {
       throw new Exception();
     }
     revertState(storedState);
   }
 
   /**
    * Revert the state of the MolecularDynamics instance to the provided MDState.
    *
    * @param state The MDState to revert to.
    */
   private void revertState(UnmodifiableState state) {
     this.state.revertState(state);
     potential.setVelocity(state.v());
     potential.setAcceleration(state.a());
     potential.setPreviousAcceleration(state.aPrevious());
     // ToDo -- move these methods into the Potential interface.
     int numberOfVariables = this.state.getNumberOfVariables();
     Atom[] atoms = molecularAssembly[0].getActiveAtomArray();
     if (atoms.length * 3 == numberOfVariables) {
       int index = 0;
       double[] x = state.x();
       double[] gradient = state.gradient();
       for (Atom atom : atoms) {
         atom.moveTo(x[index], x[index + 1], x[index + 2]);
         atom.setXYZGradient(gradient[index], gradient[index + 1], gradient[index + 2]);
         index += 3;
       }
     }
   }
 
 }