// ******************************************************************************
   //
   // 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.potential;
  
  import edu.rit.pj.IntegerForLoop;
  import edu.rit.pj.IntegerSchedule;
  import edu.rit.pj.ParallelRegion;
  import edu.rit.pj.ParallelTeam;
  import edu.rit.pj.reduction.SharedDouble;
  import ffx.crystal.Crystal;
  import ffx.crystal.CrystalPotential;
  import ffx.crystal.LatticeSystem;
  import ffx.crystal.NCSCrystal;
  import ffx.crystal.ReplicatesCrystal;
  import ffx.crystal.SpaceGroup;
  import ffx.crystal.SpaceGroupDefinitions;
  import ffx.crystal.SymOp;
  import ffx.numerics.Constraint;
  import ffx.numerics.atomic.AtomicDoubleArray.AtomicDoubleArrayImpl;
  import ffx.numerics.atomic.AtomicDoubleArray3D;
  import ffx.numerics.math.Double3;
  import ffx.numerics.switching.ConstantSwitch;
  import ffx.numerics.switching.UnivariateFunctionFactory;
  import ffx.numerics.switching.UnivariateSwitchingFunction;
  import ffx.potential.bonded.Angle;
  import ffx.potential.bonded.AngleTorsion;
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.Bond;
  import ffx.potential.bonded.BondedTerm;
  import ffx.potential.bonded.ImproperTorsion;
  import ffx.potential.bonded.LambdaInterface;
  import ffx.potential.bonded.MSNode;
  import ffx.potential.bonded.MultiResidue;
  import ffx.potential.bonded.OutOfPlaneBend;
  import ffx.potential.bonded.PiOrbitalTorsion;
  import ffx.potential.bonded.RelativeSolvation;
  import ffx.potential.bonded.RelativeSolvation.SolvationLibrary;
  import ffx.potential.bonded.Residue;
  import ffx.potential.bonded.RestrainDistance;
  import ffx.potential.bonded.StretchBend;
  import ffx.potential.bonded.StretchTorsion;
  import ffx.potential.bonded.Torsion;
  import ffx.potential.bonded.TorsionTorsion;
  import ffx.potential.bonded.UreyBradley;
  import ffx.potential.constraint.CcmaConstraint;
  import ffx.potential.constraint.SettleConstraint;
  import ffx.potential.extended.ExtendedSystem;
  import ffx.potential.nonbonded.COMRestraint;
  import ffx.potential.nonbonded.GeneralizedKirkwood;
  import ffx.potential.nonbonded.NCSRestraint;
  import ffx.potential.nonbonded.ParticleMeshEwald;
  import ffx.potential.nonbonded.RestrainGroups;
  import ffx.potential.bonded.RestrainPosition;
  import ffx.potential.nonbonded.VanDerWaals;
  import ffx.potential.nonbonded.VanDerWaalsTornado;
  import ffx.potential.openmm.OpenMMEnergy;
  import ffx.potential.parameters.AngleType;
  import ffx.potential.parameters.AngleType.AngleMode;
  import ffx.potential.parameters.BondType;
  import ffx.potential.parameters.ForceField;
  import ffx.potential.parameters.ForceField.ELEC_FORM;
  import ffx.potential.parameters.OutOfPlaneBendType;
  import ffx.potential.parameters.TorsionType;
  import ffx.potential.utils.ConvexHullOps;
 import ffx.potential.utils.EnergyException;
 import ffx.potential.utils.PotentialsFunctions;
 import ffx.potential.utils.PotentialsUtils;
 import ffx.utilities.FFXProperty;
 import org.apache.commons.configuration2.CompositeConfiguration;
 
 import javax.annotation.Nullable;
 import java.io.File;
 import java.time.LocalDateTime;
 import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_NmPerAngstrom;
 import static ffx.potential.bonded.BondedTerm.removeNeuralNetworkTerms;
 import static ffx.potential.bonded.RestrainPosition.parseRestrainPositions;
 import static ffx.potential.nonbonded.VanDerWaalsForm.DEFAULT_VDW_CUTOFF;
 import static ffx.potential.nonbonded.pme.EwaldParameters.DEFAULT_EWALD_CUTOFF;
 import static ffx.potential.parameters.ForceField.toEnumForm;
 import static ffx.potential.parsers.XYZFileFilter.isXYZ;
 import static ffx.utilities.PropertyGroup.NonBondedCutoff;
 import static ffx.utilities.PropertyGroup.PotentialFunctionSelection;
 import static java.lang.Double.isInfinite;
 import static java.lang.Double.isNaN;
 import static java.lang.String.format;
 import static java.lang.System.arraycopy;
 import static java.util.Arrays.sort;
 import static org.apache.commons.io.FilenameUtils.removeExtension;
 import static org.apache.commons.math3.util.FastMath.PI;
 import static org.apache.commons.math3.util.FastMath.max;
 import static org.apache.commons.math3.util.FastMath.min;
 import static org.apache.commons.math3.util.FastMath.sqrt;
 
 /**
  * Compute the potential energy and derivatives of a molecular system described by a force field.
  *
  * @author Michael J. Schnieders
  * @since 1.0
  */
 public class ForceFieldEnergy implements CrystalPotential, LambdaInterface {
 
   /**
    * Default tolerance for numerical methods of solving constraints.
    */
   public static final double DEFAULT_CONSTRAINT_TOLERANCE = 1E-4;
   /**
    * A Logger for the ForceFieldEnergy class.
    */
   private static final Logger logger = Logger.getLogger(ForceFieldEnergy.class.getName());
   /**
    * Convert from nanoseconds to seconds.
    */
   private static final double toSeconds = 1.0e-9;
   /**
    * The MolecularAssembly associated with this force field energy.
    */
   protected final MolecularAssembly molecularAssembly;
   /**
    * If the absolute value of a gradient component is greater than "maxDebugGradient", verbose
    * logging results.
    */
   public final double maxDebugGradient;
   /**
    * The Parallel Java ParallelTeam instance.
    */
   private final ParallelTeam parallelTeam;
   /**
    * An NCS restraint term.
    */
   private final NCSRestraint ncsRestraint;
   /**
    * A Center-of-Mass restraint term.
    */
   private final COMRestraint comRestraint;
   /**
    * Non-Bonded van der Waals energy.
    */
   private final VanDerWaals vanderWaals;
   /**
    * ANI2x Neutral Network Potential.
    */
   private final ANIEnergy aniEnergy;
   private final List<Constraint> constraints;
 
   /**
    * RestrainMode specifies how restrain terms are applied for dual topology calculations.
    */
   public enum RestrainMode {
     /**
      * Restrain terms are applied with the energy.
      */
     ENERGY,
     /**
      * Restrain terms are applied with the alchemical restraints (Lambda Bonded Terms).
      */
     ALCHEMICAL
   }
 
   @FFXProperty(name = "vdw-cutoff", propertyGroup = NonBondedCutoff, defaultValue = "12.0", description = """
       Sets the cutoff distance value in Angstroms for van der Waals potential energy interactions.
       The energy for any pair of van der Waals sites beyond the cutoff distance will be set to zero.
       Other properties can be used to define the smoothing scheme near the cutoff distance.
       The default cutoff distance in the absence of the vdw-cutoff keyword is infinite for nonperiodic
       systems and 12.0 for periodic systems.
       """)
   private double vdwCutoff;
 
   @FFXProperty(name = "ewald-cutoff", propertyGroup = NonBondedCutoff, defaultValue = "7.0", description = """
       Sets the value in Angstroms of the real-space distance cutoff for use during Ewald summation.
       By default, in the absence of the ewald-cutoff property, a value of 7.0 is used.
       """)
   private double ewaldCutoff;
 
   @FFXProperty(name = "gk-cutoff", propertyGroup = NonBondedCutoff, defaultValue = "12.0", description = """
       Sets the value in Angstroms of the generalized Kirkwood distance cutoff for use
       during implicit solvent simulations. By default, in the absence of the gk-cutoff property,
       no cutoff is used under aperiodic boundary conditions and the vdw-cutoff is used under PBC.
       """)
   private double gkCutoff;
 
   private static final double DEFAULT_LIST_BUFFER = 2.0;
 
   @FFXProperty(name = "list-buffer", propertyGroup = NonBondedCutoff, defaultValue = "2.0", description = """
       Sets the size of the neighbor list buffer in Angstroms for potential energy functions.
       This value is added to the actual cutoff distance to determine which pairs will be kept on the neighbor list.
       This buffer value is used for all potential function neighbor lists.
       The default value in the absence of the list-buffer keyword is 2.0 Angstroms.
       """)
   private double listBuffer;
 
   /**
    * 2.0 times the neighbor list cutoff.
    */
   private final double cutOff2;
   /**
    * The non-bonded cut-off plus buffer distance (Angstroms).
    */
   private final double cutoffPlusBuffer;
   /**
    * Particle-Mesh Ewald electrostatic energy.
    */
   private final ParticleMeshEwald particleMeshEwald;
   /**
    * The Electrostatic functional form.
    */
   private final ELEC_FORM elecForm;
   /**
    * Original state of the neural network energy term flag.
    */
   private final boolean nnTermOrig;
   /**
    * Original state of the Bond energy term flag.
    */
   private final boolean bondTermOrig;
   /**
    * Original state of the Angle energy term flag.
    */
   private final boolean angleTermOrig;
   /**
    * Original state of the Stretch-Bend energy term flag.
    */
   private final boolean stretchBendTermOrig;
   /**
    * Original state of the Urey-Bradley energy term flag.
    */
   private final boolean ureyBradleyTermOrig;
   /**
    * Original state of the Out-of-Plane Bend energy term flag.
    */
   private final boolean outOfPlaneBendTermOrig;
   /**
    * Original state of the Torsion energy term flag.
    */
   private final boolean torsionTermOrig;
   /**
    * Original state of the Stretch-Torsion energy term flag.
    */
   private final boolean stretchTorsionTermOrig;
   /**
    * Original state of the Angle-Torsion energy term flag.
    */
   private final boolean angleTorsionTermOrig;
   /**
    * Original state of the Improper Torsion energy term flag.
    */
   private final boolean improperTorsionTermOrig;
   /**
    * Original state of the Pi-Orbital Torsion energy term flag.
    */
   private final boolean piOrbitalTorsionTermOrig;
   /**
    * Original state of the Torsion-Torsion energy term flag.
    */
   private final boolean torsionTorsionTermOrig;
   /**
    * Original state of the RestrainPosition term flag.
    */
   private final boolean restrainPositionTermOrig;
   /**
    * Original state of the RestrainGroup term flag.
    */
   private final boolean restrainGroupTermOrig;
   /**
    * Original state of the RestrainDistance term flag.
    */
   private final boolean restrainDistanceTermOrig;
   /**
    * Original state of the RestrainTorsion term flag.
    */
   private final boolean restrainTorsionTermOrig;
 
   /**
    * Original state of the van der Waals energy term flag.
    */
   private final boolean vanderWaalsTermOrig;
   /**
    * Original state of the multipole energy term flag.
    */
   private final boolean multipoleTermOrig;
   /**
    * Original state of the polarization energy term flag.
    */
   private final boolean polarizationTermOrig;
   /**
    * Original state of the GK energy term flag.
    */
   private final boolean generalizedKirkwoodTermOrig;
 
   private boolean esvTermOrig;
   /**
    * Flag to indicate hydrogen bonded terms should be scaled up.
    */
   private final boolean rigidHydrogens;
   /**
    * Indicates application of lambda scaling to all Torsion based energy terms.
    */
   private final boolean lambdaTorsions;
   /**
    * Relative solvation term (TODO: needs further testing).
    */
   private final RelativeSolvation relativeSolvation;
   private final boolean relativeSolvationTerm;
   private final Platform platform = Platform.FFX;
 
   /**
    * Indicates use of the Lambda state variable.
    */
   @FFXProperty(name = "lambdaterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "false", description = "Specifies use of the Lambda state variable.")
   protected boolean lambdaTerm;
   /**
    * Current value of the Lambda state variable.
    */
   private double lambda = 1.0;
   /**
    * Optimization scaling value to use for each degree of freedom.
    */
   protected double[] optimizationScaling = null;
   /**
    * Indicates only bonded energy terms effected by Lambda should be evaluated.
    */
   public boolean lambdaBondedTerms = false;
   /**
    * Indicates all bonded energy terms should be evaluated if lambdaBondedTerms is true.
    */
   boolean lambdaAllBondedTerms = false;
 
   /**
    * Flag to indicate proper shutdown of the ForceFieldEnergy.
    */
   boolean destroyed = false;
   /**
    * An instance of the STATE enumeration to specify calculation of slowly varying energy terms, fast
    * varying or both.
    */
   private STATE state = STATE.BOTH;
   /**
    * The array of Atoms being evaluated.
    */
   private final Atom[] atoms;
   /**
    * An array of Bond terms.
    */
   private final Bond[] bonds;
   /**
    * An array of Angle terms.
    */
   private final Angle[] angles;
   /**
    * An array of Stretch-Bend terms.
    */
   private final StretchBend[] stretchBends;
   /**
    * An array of Urey-Bradley terms.
    */
   private final UreyBradley[] ureyBradleys;
   /**
    * An array of Out of Plane Bend terms.
    */
   private final OutOfPlaneBend[] outOfPlaneBends;
   /**
    * An array of Torsion terms.
    */
   private final Torsion[] torsions;
   /**
    * An array of Improper Torsion terms.
    */
   private final ImproperTorsion[] improperTorsions;
   /**
    * An array of Pi-Orbital Torsion terms.
    */
   private final PiOrbitalTorsion[] piOrbitalTorsions;
   /**
    * An array of Torsion-Torsion terms.
    */
   private final TorsionTorsion[] torsionTorsions;
   /**
    * An array of Stretch-Torsion terms.
    */
   private final StretchTorsion[] stretchTorsions;
   /**
    * An array of Angle-Torsion terms.
    */
   private final AngleTorsion[] angleTorsions;
 
   /**
    * An array of Restrain Distance terms.
    */
   private RestrainDistance[] restrainDistances;
   /**
    * An array of Restrain Torsion terms.
    */
   private Torsion[] restrainTorsions;
   /**
    * An array of Restrain Position terms.
    */
   private final RestrainPosition[] restrainPositions;
   /**
    * The Restrain Groups energy term.
    */
   private final RestrainGroups restrainGroups;
   /**
    * RestrainMode specifies how restrain terms are applied for dual topology calculations.
    */
   private final RestrainMode restrainMode;
 
   /**
    * Number of atoms in the system.
    */
   private final int nAtoms;
   /**
    * Number of bond terms in the system.
    */
   private final int nBonds;
   /**
    * Number of angle terms in the system.
    */
   private final int nAngles;
   /**
    * Number of stretch-bend terms in the system.
    */
   private final int nStretchBends;
   /**
    * Number of Urey-Bradley terms in the system.
    */
   private final int nUreyBradleys;
   /**
    * Number of Out of Plane Bend terms in the system.
    */
   private final int nOutOfPlaneBends;
   /**
    * Number of Torsion terms in the system.
    */
   private final int nTorsions;
   /**
    * Number of Improper Torsion terms in the system.
    */
   private final int nImproperTorsions;
   /**
    * Number of Pi-Orbital Torsion terms in the system.
    */
   private final int nPiOrbitalTorsions;
   /**
    * Number of Torsion-Torsion terms in the system.
    */
   private final int nTorsionTorsions;
   /**
    * Number of Angle-Torsion terms in the system.
    */
   private final int nAngleTorsions;
   /**
    * Number of Stretch-Torsion terms in the system.
    */
   private final int nStretchTorsions;
 
   /**
    * Number of RestrainDistance terms in the system.
    */
   private int nRestrainDistances;
   /**
    * Number of RestraintTorsion terms in the system.
    */
   private int nRestrainTorsions;
   /**
    * Number of Restrain Positions in the system.
    */
   private int nRestrainPositions;
   /**
    * Number of Restrain Groups in the system.
    */
   private int nRestrainGroups;
 
   /**
    * Number of van der Waals interactions evaluated.
    */
   private int nVanDerWaalInteractions;
   /**
    * Number of electrostatic interactions evaluated.
    */
   private int nPermanentInteractions;
   /**
    * Number of implicit solvent interactions evaluated.
    */
   private int nGKInteractions;
 
   /**
    * The boundary conditions used when evaluating the force field energy.
    */
   private Crystal crystal;
   /**
    * A Parallel Java Region used to evaluate Bonded energy values.
    */
   private final BondedRegion bondedRegion;
 
   /**
    * Specifies use of an intramolecular neural network.
    */
   private boolean nnTerm;
 
   /**
    * Specifies use of the bond stretch potential.
    */
   @FFXProperty(name = "bondterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "true", description = "Specifies use of the bond stretch potential.")
   private boolean bondTerm;
 
   /**
    * Specifies use of the angle bend potential.
    */
   @FFXProperty(name = "angleterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "true", description = "Specifies use of the angle bend potential.")
   private boolean angleTerm;
 
   /**
    * Evaluate Stretch-Bend energy terms.
    */
   @FFXProperty(name = "strbndterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "true", description = "Specifies use of the stretch-bend potential.")
   private boolean stretchBendTerm;
 
   /**
    * Evaluate Urey-Bradley energy terms.
    */
   @FFXProperty(name = "ureyterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "true", description = "Specifies use of the Urey-Bradley potential.")
   private boolean ureyBradleyTerm;
 
   /**
    * Evaluate Out of Plane Bend energy terms.
    */
   @FFXProperty(name = "opbendterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "true", description = "Specifies use of the out-of-plane potential.")
   private boolean outOfPlaneBendTerm;
 
   /**
    * Evaluate Torsion energy terms.
    */
   @FFXProperty(name = "torsionterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "true", description = "Specifies use of the torsional potential.")
   private boolean torsionTerm;
 
   /**
    * Evaluate Stretch-Torsion energy terms.
    */
   @FFXProperty(name = "strtorterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "true", description = "Specifies use of the stretch-torsion potential.")
   private boolean stretchTorsionTerm;
 
   /**
    * Evaluate Angle-Torsion energy terms.
    */
   @FFXProperty(name = "angtorterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "true", description = "Specifies use of the angle-torsion potential.")
   private boolean angleTorsionTerm;
 
   /**
    * Evaluate Improper Torsion energy terms.
    */
   @FFXProperty(name = "imptorterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "true", description = "Specifies use of the improper torsion potential.")
   private boolean improperTorsionTerm;
 
   /**
    * Evaluate Pi-Orbital Torsion energy terms.
    */
   @FFXProperty(name = "pitorsterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "true", description = "Specifies use of the pi-system torsion potential.")
   private boolean piOrbitalTorsionTerm;
 
   /**
    * Evaluate Torsion-Torsion energy terms.
    */
   @FFXProperty(name = "tortorterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "true", description = "Specifies use of the pi-system torsion potential.")
   private boolean torsionTorsionTerm;
 
   /**
    * Evaluate van der Waals energy term.
    */
   @FFXProperty(name = "vdwterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "true", description = """
       Specifies use of the vdw der Waals potential.
       If set to false, all non-bonded terms are turned off.
       """)
   private boolean vanderWaalsTerm;
 
   /**
    * Evaluate permanent multipole electrostatics energy term.
    */
   @FFXProperty(name = "mpoleterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "true", description = """
       Specifies use of the fixed charge electrostatic potential.
       Setting mpoleterm to false also turns off polarization and generalized Kirkwood,
       overriding the polarizeterm and gkterm properties.
       """)
   private boolean multipoleTerm;
 
   /**
    * Evaluate polarization energy term.
    */
   @FFXProperty(name = "polarizeterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "true", description = """
       Specifies use of the polarizable electrostatic potential.
       Setting polarizeterm to false overrides the polarization property.
       """)
   private boolean polarizationTerm;
 
   /**
    * Evaluate generalized Kirkwood energy term.
    */
   @FFXProperty(name = "gkterm", clazz = Boolean.class, propertyGroup = PotentialFunctionSelection,
       defaultValue = "false", description = "Specifies use of generalized Kirkwood electrostatics.")
   private boolean generalizedKirkwoodTerm;
 
   /**
    * Evaluate COM energy term.
    */
   private boolean comTerm;
   /**
    * Original state of the COM energy term flag.
    */
   private boolean comTermOrig;
   /**
    * Evaluate NCS energy term.
    */
   private boolean ncsTerm;
   /**
    * Original state of the NCS energy term flag.
    */
   private boolean ncsTermOrig;
   /**
    * Evaluate RestrainDistance terms.
    */
   private boolean restrainDistanceTerm;
   /**
    * Evaluate RestrainTorsion terms.
    */
   private boolean restrainTorsionTerm;
   /**
    * Evaluate RestrainPosition term.
    */
   private boolean restrainPositionTerm;
   /**
    * Evaluate RestrainGroup terms.
    */
   private boolean restrainGroupTerm;
 
   /**
    * Scale factor for increasing the strength of bonded terms involving hydrogen atoms.
    */
   private double rigidScale;
 
   /**
    * The total neutral network energy.
    */
   private double nnEnergy;
   /**
    * The total Bond term energy.
    */
   private double bondEnergy;
   /**
    * The RMSD of all Bond distances relative to their equilibrium values.
    */
   private double bondRMSD;
   /**
    * The total Angle term energy.
    */
   private double angleEnergy;
   /**
    * The RMSD of all Angle bends relative to their equilibrium values.
    */
   private double angleRMSD;
   /**
    * The total Stretch-Bend term energy.
    */
   private double stretchBendEnergy;
   /**
    * The total Urey-Bradley term energy.
    */
   private double ureyBradleyEnergy;
   /**
    * The total Out-of-Plane term energy.
    */
   private double outOfPlaneBendEnergy;
   /**
    * The total Torsion term energy.
    */
   private double torsionEnergy;
   /**
    * The total Stretch-Torsion term energy.
    */
   private double stretchTorsionEnergy;
   /**
    * The total Angle-Torsion term energy.
    */
   private double angleTorsionEnergy;
   /**
    * The total Improper Torsion term energy.
    */
   private double improperTorsionEnergy;
   /**
    * The total Pi-Orbital Torsion term energy.
    */
   private double piOrbitalTorsionEnergy;
   /**
    * The total Torsion-Torsion term energy.
    */
   private double torsionTorsionEnergy;
 
   /**
    * The total RestrainDistance energy.
    */
   private double restrainDistanceEnergy;
   /**
    * The RestrainPosition Energy.
    */
   private double restrainPositionEnergy;
   /**
    * The RestrainGroup Energy.
    */
   private double restrainGroupEnergy;
   /**
    * The RestrainTorsion Energy.
    */
   private double restrainTorsionEnergy;
 
   /**
    * The total energy for all Bonded Energy terms.
    */
   private double totalBondedEnergy;
   /**
    * The total van der Waals energy.
    */
   private double vanDerWaalsEnergy;
   /**
    * The permanent Multipole energy.
    */
   private double permanentMultipoleEnergy;
   /**
    * The permanent multipole real space energy.
    */
   private double permanentRealSpaceEnergy;
   /**
    * The total polarization energy.
    */
   private double polarizationEnergy;
   /**
    * The total electrostatic energy.
    */
   private double totalMultipoleEnergy;
   /**
    * The total non-bonded energy (van der Waals plus electrostatic).
    */
   private double totalNonBondedEnergy;
   /**
    * The solvation energy (GK).
    */
   private double solvationEnergy;
   /**
    * The total NCS Energy.
    */
   private double ncsEnergy;
 
   /**
    * The total COM Restraint Energy.
    */
   private double comRestraintEnergy;
   /**
    * The total system energy.
    */
   private double totalEnergy;
 
   /**
    * Time to evaluate the neutral network.
    */
   private long nnTime;
   /**
    * Time to evaluate Bond terms.
    */
   private long bondTime;
   /**
    * Time to evaluate Angle terms.
    */
   private long angleTime;
   /**
    * Time to evaluate Stretch-Bend terms.
    */
   private long stretchBendTime;
   /**
    * Time to evaluate Urey-Bradley terms.
    */
   private long ureyBradleyTime;
   /**
    * Time to evaluate Out-Of-Plane Bend terms.
    */
   private long outOfPlaneBendTime;
   /**
    * Time to evaluate Torsion terms.
    */
   private long torsionTime;
   /**
    * Time to evaluate Angle-Torsion terms.
    */
   private long angleTorsionTime;
   /**
    * Time to evaluate Stretch-Torsion terms.
    */
   private long stretchTorsionTime;
   /**
    * Time to evaluate Pi-Orbital Torsion terms.
    */
   private long piOrbitalTorsionTime;
   /**
    * Time to evaluate Improper Torsion terms.
    */
   private long improperTorsionTime;
   /**
    * Time to evaluate Torsion-Torsion terms.
    */
   private long torsionTorsionTime;
   /**
    * Time to evaluate van der Waals term.
    */
   private long vanDerWaalsTime;
   /**
    * Time to evaluate electrostatics term.
    */
   private long electrostaticTime;
   /**
    * Time to evaluate RestrainDistance terms.
    */
   private long restrainDistanceTime;
   /**
    * Time to evaluate RestrainTorsion terms.
    */
   private long restrainTorsionTime;
 
   /**
    * Time to evaluate Center of Mass restraint term.
    */
   private long comRestraintTime;
   /**
    * Time to evaluate restrain group term.
    */
   private long restrainGroupTime;
   /**
    * Time to evaluate all energy terms.
    */
   private long totalTime;
 
   /**
    * Constant pH extended system (TODO: needs further testing).
    */
   private ExtendedSystem esvSystem = null;
 
   private boolean esvTerm;
   private double esvBias;
   /**
    * Time to evaluate NCS term.
    */
   private long ncsTime;
   private int nRelativeSolvations;
   /**
    * Time to evaluate coordinate restraint term.
    */
   private long restrainPositionTime;
 
   private double relativeSolvationEnergy;
   /**
    * Enable verbose printing if large energy gradient components are observed.
    */
   private boolean printOnFailure;
 
   /**
    * Constructor for ForceFieldEnergy.
    *
    * @param molecularAssembly a {@link ffx.potential.MolecularAssembly} object.
    */
   protected ForceFieldEnergy(MolecularAssembly molecularAssembly) {
     this(molecularAssembly, ParallelTeam.getDefaultThreadCount());
   }
 
   /**
    * Constructor for ForceFieldEnergy.
    *
    * @param molecularAssembly a {@link ffx.potential.MolecularAssembly} object.
    * @param numThreads        a int.
    */
   protected ForceFieldEnergy(MolecularAssembly molecularAssembly, int numThreads) {
     // Get a reference to the sorted atom array.
     this.molecularAssembly = molecularAssembly;
     atoms = molecularAssembly.getAtomArray();
     nAtoms = atoms.length;
 
     // Check that atom ordering is correct and count the number of active atoms.
     for (int i = 0; i < nAtoms; i++) {
       int index = atoms[i].getXyzIndex() - 1;
       assert (i == index);
     }
 
     // Enforce that the number of threads be less than or equal to the number of atoms.
     int nThreads = min(nAtoms, numThreads);
     parallelTeam = new ParallelTeam(nThreads);
 
     ForceField forceField = molecularAssembly.getForceField();
     CompositeConfiguration properties = forceField.getProperties();
     String name = forceField.toString().toUpperCase();
 
     logger.info(format(" Constructing Force Field %s", name));
     logger.info(format("\n SMP threads:                        %10d", nThreads));
 
     // Rename water protons if requested.
     boolean standardizeAtomNames = properties.getBoolean("standardizeAtomNames", true);
     if (standardizeAtomNames) {
       molecularAssembly.renameWaterProtons();
     }
 
     nnTerm = forceField.getBoolean("NNTERM", false);
     // For now, all atoms are neural network atoms, or none are.
     if (nnTerm) {
       for (Atom atom : atoms) {
         atom.setNeuralNetwork(true);
       }
     }
     bondTerm = forceField.getBoolean("BONDTERM", true);
     angleTerm = forceField.getBoolean("ANGLETERM", true);
     stretchBendTerm = forceField.getBoolean("STRBNDTERM", true);
     ureyBradleyTerm = forceField.getBoolean("UREYTERM", true);
     outOfPlaneBendTerm = forceField.getBoolean("OPBENDTERM", true);
     torsionTerm = forceField.getBoolean("TORSIONTERM", true);
     stretchTorsionTerm = forceField.getBoolean("STRTORTERM", true);
     angleTorsionTerm = forceField.getBoolean("ANGTORTERM", true);
     piOrbitalTorsionTerm = forceField.getBoolean("PITORSTERM", true);
     torsionTorsionTerm = forceField.getBoolean("TORTORTERM", true);
     improperTorsionTerm = forceField.getBoolean("IMPROPERTERM", true);
     vanderWaalsTerm = forceField.getBoolean("VDWTERM", true);
 
     boolean tornadoVM = forceField.getBoolean("tornado", false);
     if (vanderWaalsTerm && !tornadoVM) {
       multipoleTerm = forceField.getBoolean("MPOLETERM", true);
       if (multipoleTerm) {
         String polarizeString = forceField.getString("POLARIZATION", "NONE");
         boolean defaultPolarizeTerm = !polarizeString.equalsIgnoreCase("NONE");
         polarizationTerm = forceField.getBoolean("POLARIZETERM", defaultPolarizeTerm);
         generalizedKirkwoodTerm = forceField.getBoolean("GKTERM", false);
       } else {
         // If multipole electrostatics is turned off, turn off all electrostatics.
         polarizationTerm = false;
         generalizedKirkwoodTerm = false;
       }
     } else {
       // If van der Waals is turned off, turn off all non-bonded terms.
       multipoleTerm = false;
       polarizationTerm = false;
       generalizedKirkwoodTerm = false;
     }
 
 
     lambdaTerm = forceField.getBoolean("LAMBDATERM", false);
     comTerm = forceField.getBoolean("COMRESTRAINTERM", false);
     lambdaTorsions = forceField.getBoolean("TORSION_LAMBDATERM", false);
     printOnFailure = forceField.getBoolean("PRINT_ON_FAILURE", false);
 
     // Detect "restrain-distance" property.
     if (properties.containsKey("restrain-distance")) {
       restrainDistanceTerm = true;
     } else {
       restrainDistanceTerm = false;
     }
 
     // Detect "restrain-torsion" property.
     if (properties.containsKey("restrain-torsion")) {
       restrainTorsionTerm = true;
     } else {
       restrainTorsionTerm = false;
     }
 
     String mode = forceField.getString("RESTRAIN_MODE", "ENERGY");
     if (mode.equalsIgnoreCase("ALCHEMICAL")) {
       restrainMode = RestrainMode.ALCHEMICAL;
     } else {
       restrainMode = RestrainMode.ENERGY;
     }
     if (restrainTorsionTerm) {
       logger.info(" Restrain Torsion Mode: " + restrainMode);
     }
 
     // Detect "restrain-groups" property.
     if (properties.containsKey("restrain-groups")) {
       restrainGroupTerm = true;
     } else {
       restrainGroupTerm = false;
     }
 
     // Detect "restrain-position" property.
     if (properties.containsKey("restrain-position") || properties.containsKey("restrain-position-lambda")) {
       restrainPositionTerm = true;
     } else {
       restrainPositionTerm = false;
     }
 
 
     // For RESPA
     nnTermOrig = nnTerm;
     bondTermOrig = bondTerm;
     angleTermOrig = angleTerm;
     stretchBendTermOrig = stretchBendTerm;
     ureyBradleyTermOrig = ureyBradleyTerm;
     outOfPlaneBendTermOrig = outOfPlaneBendTerm;
     torsionTermOrig = torsionTerm;
     angleTorsionTermOrig = angleTorsionTerm;
     stretchTorsionTermOrig = stretchTorsionTerm;
     improperTorsionTermOrig = improperTorsionTerm;
     piOrbitalTorsionTermOrig = piOrbitalTorsionTerm;
     torsionTorsionTermOrig = torsionTorsionTerm;
     vanderWaalsTermOrig = vanderWaalsTerm;
     multipoleTermOrig = multipoleTerm;
     polarizationTermOrig = polarizationTerm;
     generalizedKirkwoodTermOrig = generalizedKirkwoodTerm;
     ncsTermOrig = ncsTerm;
     comTermOrig = comTerm;
     restrainDistanceTermOrig = restrainDistanceTerm;
     restrainTorsionTermOrig = restrainTorsionTerm;
     restrainPositionTermOrig = restrainPositionTerm;
     restrainGroupTermOrig = restrainGroupTerm;
 
     // Determine the unit cell dimensions and space group.
     String spacegroup;
     double a, b, c, alpha, beta, gamma;
     boolean aperiodic;
     try {
       spacegroup = forceField.getString("SPACEGROUP", "P 1");
       SpaceGroup sg = SpaceGroupDefinitions.spaceGroupFactory(spacegroup);
       LatticeSystem latticeSystem = sg.latticeSystem;
       a = forceField.getDouble("A_AXIS");
       aperiodic = false;
       b = forceField.getDouble("B_AXIS", latticeSystem.getDefaultBAxis(a));
       c = forceField.getDouble("C_AXIS", latticeSystem.getDefaultCAxis(a, b));
       alpha = forceField.getDouble("ALPHA", latticeSystem.getDefaultAlpha());
       beta = forceField.getDouble("BETA", latticeSystem.getDefaultBeta());
       gamma = forceField.getDouble("GAMMA", latticeSystem.getDefaultGamma());
       if (!sg.latticeSystem.validParameters(a, b, c, alpha, beta, gamma)) {
         logger.severe(" Check lattice parameters.");
       }
       if (a == 1.0 && b == 1.0 && c == 1.0) {
         String message = " A-, B-, and C-axis values equal to 1.0.";
         logger.info(message);
         throw new Exception(message);
       }
       if (a <= 0.0 || b <= 0.0 || c <= 0.0 || alpha <= 0.0 || beta <= 0.0 || gamma <= 0.0) {
         // Parameters are not valid. Switch to aperiodic.
         String message = " Crystal parameters are not valid due to negative or zero value.";
         logger.warning(message);
         throw new Exception(message);
       }
     } catch (Exception e) {
       aperiodic = true;
 
       // Determine the maximum separation between atoms.
       double maxR = 0.0;
       if (nAtoms < 10) {
         for (int i = 0; i < nAtoms - 1; i++) {
           Double3 xi = atoms[i].getXYZ();
           for (int j = 1; j < nAtoms; j++) {
             double r = atoms[j].getXYZ().dist(xi);
             maxR = max(r, maxR);
           }
         }
       } else {
         try {
           maxR = ConvexHullOps.maxDist(ConvexHullOps.constructHull(atoms));
         } catch (Exception ex) {
           // If Convex Hull approach fails (e.g., coplanar input, brute force...
           logger.info(" Convex Hull operation failed with message " + ex + "\n Trying brute force approach...");
           if (logger.isLoggable(Level.FINE)) {
             logger.fine(Utilities.stackTraceToString(ex));
           }
           for (int i = 0; i < nAtoms - 1; i++) {
             Double3 xi = atoms[i].getXYZ();
             for (int j = 1; j < nAtoms; j++) {
               double r = atoms[j].getXYZ().dist(xi);
               maxR = max(r, maxR);
             }
           }
         }
       }
       maxR = max(10.0, maxR);
 
       logger.info(format(" The system will be treated as aperiodic (max separation = %6.1f A).", maxR));
 
       // Turn off reciprocal space calculations.
       forceField.addProperty("EWALD_ALPHA", "0.0");
 
       // Specify some dummy values for the crystal.
       spacegroup = "P1";
       a = 2.0 * maxR;
       b = 2.0 * maxR;
       c = 2.0 * maxR;
       alpha = 90.0;
       beta = 90.0;
       gamma = 90.0;
     }
     Crystal unitCell = new Crystal(a, b, c, alpha, beta, gamma, spacegroup);
     unitCell.setAperiodic(aperiodic);
 
     // First set cutoffs assuming PBC.
     vdwCutoff = DEFAULT_VDW_CUTOFF;
     ewaldCutoff = DEFAULT_EWALD_CUTOFF;
     gkCutoff = vdwCutoff;
     if (unitCell.aperiodic()) {
       // Default to no cutoffs for aperiodic systems.
       vdwCutoff = Double.POSITIVE_INFINITY;
       ewaldCutoff = Double.POSITIVE_INFINITY;
       gkCutoff = Double.POSITIVE_INFINITY;
     }
     // Load user specified cutoffs.
     vdwCutoff = forceField.getDouble("VDW_CUTOFF", vdwCutoff);
     ewaldCutoff = forceField.getDouble("EWALD_CUTOFF", ewaldCutoff);
     gkCutoff = forceField.getDouble("GK_CUTOFF", gkCutoff);
 
     // Neighbor list cutoff is the maximum of the vdW, Ewald and GK cutoffs (i.e. to use a single list).
     double nlistCutoff = vdwCutoff;
     if (multipoleTerm) {
       nlistCutoff = max(vdwCutoff, ewaldCutoff);
     }
     if (generalizedKirkwoodTerm) {
       nlistCutoff = max(nlistCutoff, gkCutoff);
     }
 
     // Check for a frozen neighbor list.
     boolean disabledNeighborUpdates = forceField.getBoolean("DISABLE_NEIGHBOR_UPDATES", false);
     if (disabledNeighborUpdates) {
       logger.info(format(" Neighbor list updates disabled; interactions will "
           + "only be calculated between atoms that started the simulation "
           + "within a radius of %9.3g Angstroms of each other.", nlistCutoff));
       // The individual cutoffs are infinity (i.e. they are limited by interactions in the list).
       vdwCutoff = Double.POSITIVE_INFINITY;
       ewaldCutoff = Double.POSITIVE_INFINITY;
       gkCutoff = Double.POSITIVE_INFINITY;
     }
 
     listBuffer = forceField.getDouble("LIST_BUFFER", DEFAULT_LIST_BUFFER);
     cutoffPlusBuffer = nlistCutoff + listBuffer;
     cutOff2 = 2.0 * cutoffPlusBuffer;
     unitCell = configureNCS(forceField, unitCell);
 
     // If necessary, create a ReplicatesCrystal.
     if (!aperiodic) {
       this.crystal = ReplicatesCrystal.replicatesCrystalFactory(unitCell, cutOff2);
       logger.info(format("\n Density:                                %6.3f (g/cc)",
           crystal.getDensity(molecularAssembly.getMass())));
       logger.info(crystal.toString());
     } else {
       this.crystal = unitCell;
     }
 
     if (!unitCell.aperiodic() && unitCell.spaceGroup.number == 1) {
       ncsTerm = forceField.getBoolean("NCSTERM", false);
       ncsTermOrig = ncsTerm;
     } else {
       ncsTerm = false;
       ncsTermOrig = false;
     }
 
     // Now that the crystal is set, check for special positions.
     int nSpecial = checkForSpecialPositions(forceField);
 
     rigidHydrogens = forceField.getBoolean("RIGID_HYDROGENS", false);
     rigidScale = forceField.getDouble("RIGID_SCALE", 10.0);
 
     nRelativeSolvations = 0;
     String relSolvLibrary = forceField.getString("RELATIVE_SOLVATION", "NONE").toUpperCase();
     SolvationLibrary library = SolvationLibrary.valueOf(relSolvLibrary);
     if (library == SolvationLibrary.AUTO) {
       if (generalizedKirkwoodTerm && name.toUpperCase().contains("OPLS")) {
         library = SolvationLibrary.MACCALLUM_TIP4P;
         // Change when we have good Generalized Born numbers of our own for OPLS.
       } else if (generalizedKirkwoodTerm) {
         library = SolvationLibrary.GK;
       } else {
         library = SolvationLibrary.NONE;
       }
     }
     if (library != SolvationLibrary.NONE) {
       relativeSolvationTerm = true;
       relativeSolvation = new RelativeSolvation(library, forceField);
     } else {
       relativeSolvationTerm = false;
       relativeSolvation = null;
     }
 
     boolean checkAllNodeCharges = forceField.getBoolean("CHECK_ALL_NODE_CHARGES", false);
 
     if (rigidScale <= 1.0) {
       rigidScale = 1.0;
     }
 
     logger.info("\n Bonded Terms");
     if (rigidHydrogens && rigidScale > 1.0) {
       logger.info(format("  Rigid hydrogens:                   %10.2f", rigidScale));
     }
 
     // Collect, count, pack and sort bonds.
     if (bondTerm) {
       List<Bond> bondList = molecularAssembly.getBondList();
       if (nnTerm) {
         removeNeuralNetworkTerms(bondList);
       }
       nBonds = bondList.size();
       bonds = bondList.toArray(new Bond[0]);
       sort(bonds);
       if (nBonds > 0) {
         logger.info(format("  Bonds:                             %10d", nBonds));
       }
     } else {
       nBonds = 0;
       bonds = null;
     }
 
     // Collect, count, pack and sort angles.
     if (angleTerm) {
       List<Angle> angleList = molecularAssembly.getAngleList();
       if (nnTerm) {
         removeNeuralNetworkTerms(angleList);
       }
       nAngles = angleList.size();
       angles = angleList.toArray(new Angle[0]);
       sort(angles);
       if (nAngles > 0) {
         logger.info(format("  Angles:                            %10d", nAngles));
       }
     } else {
       nAngles = 0;
       angles = null;
     }
 
     // Collect, count, pack and sort stretch-bends.
     if (stretchBendTerm) {
       List<StretchBend> stretchBendList = molecularAssembly.getStretchBendList();
       if (nnTerm) {
         removeNeuralNetworkTerms(stretchBendList);
       }
       nStretchBends = stretchBendList.size();
       stretchBends = stretchBendList.toArray(new StretchBend[0]);
       sort(stretchBends);
       if (nStretchBends > 0) {
         logger.info(format("  Stretch-Bends:                     %10d", nStretchBends));
       }
     } else {
       nStretchBends = 0;
       stretchBends = null;
     }
 
     // Collect, count, pack and sort Urey-Bradleys.
     if (ureyBradleyTerm) {
       List<UreyBradley> ureyBradleyList = molecularAssembly.getUreyBradleyList();
       if (nnTerm) {
         removeNeuralNetworkTerms(ureyBradleyList);
       }
       nUreyBradleys = ureyBradleyList.size();
       ureyBradleys = ureyBradleyList.toArray(new UreyBradley[0]);
       sort(ureyBradleys);
       if (nUreyBradleys > 0) {
         logger.info(format("  Urey-Bradleys:                     %10d", nUreyBradleys));
       }
     } else {
       nUreyBradleys = 0;
       ureyBradleys = null;
     }
 
     // Set a multiplier on the force constants of bonded terms containing hydrogens.
     if (rigidHydrogens) {
       if (bonds != null) {
         for (Bond bond : bonds) {
           if (bond.containsHydrogen()) {
             bond.setRigidScale(rigidScale);
           }
         }
       }
       if (angles != null) {
         for (Angle angle : angles) {
           if (angle.containsHydrogen()) {
             angle.setRigidScale(rigidScale);
           }
         }
       }
       if (stretchBends != null) {
         for (StretchBend stretchBend : stretchBends) {
           if (stretchBend.containsHydrogen()) {
             stretchBend.setRigidScale(rigidScale);
           }
         }
       }
       if (ureyBradleys != null) {
         for (UreyBradley ureyBradley : ureyBradleys) {
           if (ureyBradley.containsHydrogen()) {
             ureyBradley.setRigidScale(rigidScale);
           }
         }
       }
     }
 
     // Collect, count, pack and sort out-of-plane bends.
     if (outOfPlaneBendTerm) {
       List<OutOfPlaneBend> outOfPlaneBendList = molecularAssembly.getOutOfPlaneBendList();
       if (nnTerm) {
         removeNeuralNetworkTerms(outOfPlaneBendList);
       }
       nOutOfPlaneBends = outOfPlaneBendList.size();
       outOfPlaneBends = outOfPlaneBendList.toArray(new OutOfPlaneBend[0]);
       sort(outOfPlaneBends);
       if (nOutOfPlaneBends > 0) {
         logger.info(format("  Out-of-Plane Bends:                %10d", nOutOfPlaneBends));
       }
     } else {
       nOutOfPlaneBends = 0;
       outOfPlaneBends = null;
     }
 
     // Collect, count and pack torsions.
     if (torsionTerm) {
       List<Torsion> torsionList = molecularAssembly.getTorsionList();
       if (nnTerm) {
         removeNeuralNetworkTerms(torsionList);
       }
       nTorsions = torsionList.size();
       torsions = torsionList.toArray(new Torsion[0]);
       if (nTorsions > 0) {
         logger.info(format("  Torsions:                          %10d", nTorsions));
       }
     } else {
       nTorsions = 0;
       torsions = null;
     }
 
     // Collect, count and pack stretch torsions.
     if (stretchTorsionTerm) {
       List<StretchTorsion> stretchTorsionList = molecularAssembly.getStretchTorsionList();
       if (nnTerm) {
         removeNeuralNetworkTerms(stretchTorsionList);
       }
       nStretchTorsions = stretchTorsionList.size();
       stretchTorsions = stretchTorsionList.toArray(new StretchTorsion[0]);
       if (nStretchTorsions > 0) {
         logger.info(format("  Stretch-Torsions:                  %10d", nStretchTorsions));
       }
     } else {
       nStretchTorsions = 0;
       stretchTorsions = null;
     }
 
     // Collect, count and pack angle torsions.
     if (angleTorsionTerm) {
       List<AngleTorsion> angleTorsionList = molecularAssembly.getAngleTorsionList();
       if (nnTerm) {
         removeNeuralNetworkTerms(angleTorsionList);
       }
       nAngleTorsions = angleTorsionList.size();
       angleTorsions = angleTorsionList.toArray(new AngleTorsion[0]);
       if (nAngleTorsions > 0) {
         logger.info(format("  Angle-Torsions:                    %10d", nAngleTorsions));
       }
     } else {
       nAngleTorsions = 0;
       angleTorsions = null;
     }
 
     // Collect, count and pack pi-orbital torsions.
     if (piOrbitalTorsionTerm) {
       List<PiOrbitalTorsion> piOrbitalTorsionList = molecularAssembly.getPiOrbitalTorsionList();
       if (nnTerm) {
         removeNeuralNetworkTerms(piOrbitalTorsionList);
       }
       nPiOrbitalTorsions = piOrbitalTorsionList.size();
       piOrbitalTorsions = piOrbitalTorsionList.toArray(new PiOrbitalTorsion[0]);
       if (nPiOrbitalTorsions > 0) {
         logger.info(format("  Pi-Orbital Torsions:               %10d", nPiOrbitalTorsions));
       }
     } else {
       nPiOrbitalTorsions = 0;
       piOrbitalTorsions = null;
     }
 
     // Collect, count and pack torsion-torsions.
     if (torsionTorsionTerm) {
       List<TorsionTorsion> torsionTorsionList = molecularAssembly.getTorsionTorsionList();
       if (nnTerm) {
         removeNeuralNetworkTerms(torsionTorsionList);
       }
       nTorsionTorsions = torsionTorsionList.size();
       torsionTorsions = torsionTorsionList.toArray(new TorsionTorsion[0]);
       if (nTorsionTorsions > 0) {
         logger.info(format("  Torsion-Torsions:                  %10d", nTorsionTorsions));
       }
     } else {
       nTorsionTorsions = 0;
       torsionTorsions = null;
     }
 
     // Collect, count and pack improper torsions.
     if (improperTorsionTerm) {
       List<ImproperTorsion> improperTorsionList = molecularAssembly.getImproperTorsionList();
       if (nnTerm) {
         removeNeuralNetworkTerms(improperTorsionList);
       }
       nImproperTorsions = improperTorsionList.size();
       improperTorsions = improperTorsionList.toArray(new ImproperTorsion[0]);
       if (nImproperTorsions > 0) {
         logger.info(format("  Improper Torsions:                 %10d", nImproperTorsions));
       }
     } else {
       nImproperTorsions = 0;
       improperTorsions = null;
     }
 
     int[] molecule = molecularAssembly.getMoleculeNumbers();
     if (vanderWaalsTerm) {
       logger.info("\n Non-Bonded Terms");
       boolean[] nn = null;
       if (nnTerm) {
         nn = molecularAssembly.getNeuralNetworkIdentity();
       } else {
         nn = new boolean[nAtoms];
         Arrays.fill(nn, false);
       }
 
       if (!tornadoVM) {
         vanderWaals = new VanDerWaals(atoms, molecule, nn, crystal, forceField, parallelTeam,
             vdwCutoff, nlistCutoff);
       } else {
         vanderWaals = new VanDerWaalsTornado(atoms, crystal, forceField, vdwCutoff);
       }
     } else {
       vanderWaals = null;
     }
 
     if (nnTerm) {
       aniEnergy = new ANIEnergy(molecularAssembly);
     } else {
       aniEnergy = null;
     }
 
     if (multipoleTerm) {
       if (name.contains("OPLS") || name.contains("AMBER") || name.contains("CHARMM")) {
         elecForm = ELEC_FORM.FIXED_CHARGE;
       } else {
         elecForm = ELEC_FORM.PAM;
       }
       particleMeshEwald = new ParticleMeshEwald(atoms, molecule, forceField, crystal,
           vanderWaals.getNeighborList(), elecForm, ewaldCutoff, gkCutoff, parallelTeam);
       double charge = molecularAssembly.getCharge(checkAllNodeCharges);
       logger.info(format("\n  Overall system charge:             %10.3f", charge));
     } else {
       elecForm = null;
       particleMeshEwald = null;
     }
 
     if (ncsTerm) {
       String sg = forceField.getString("NCSGROUP", "P 1");
       Crystal ncsCrystal = new Crystal(a, b, c, alpha, beta, gamma, sg);
       ncsRestraint = new NCSRestraint(atoms, forceField, ncsCrystal);
     } else {
       ncsRestraint = null;
     }
 
     if (restrainPositionTerm) {
       restrainPositions = parseRestrainPositions(molecularAssembly);
       if (restrainPositions != null) {
         nRestrainPositions = restrainPositions.length;
       } else {
         nRestrainPositions = 0;
       }
     } else {
       restrainPositions = null;
     }
 
     if (restrainGroupTerm) {
       restrainGroups = new RestrainGroups(molecularAssembly);
       nRestrainGroups = restrainGroups.getNumberOfRestraints();
     } else {
       restrainGroups = null;
     }
 
     if (comTerm) {
       comRestraint = new COMRestraint(molecularAssembly);
     } else {
       comRestraint = null;
     }
 
     if (restrainDistanceTerm) {
       // Apply restrain-distance records.
       configureRestrainDistances(properties);
     }
 
     if (restrainTorsionTerm) {
       nRestrainTorsions = configureRestrainTorsions(properties, forceField);
     }
 
     bondedRegion = new BondedRegion();
     maxDebugGradient = forceField.getDouble("MAX_DEBUG_GRADIENT", Double.POSITIVE_INFINITY);
 
     molecularAssembly.setPotential(this);
 
     // Configure constraints.
     constraints = configureConstraints(forceField);
 
     if (lambdaTerm) {
       this.setLambda(1.0);
       if (nSpecial == 0) {
         // For lambda calculations (e.g., polymorph searches), turn-off special position checks.
         // In this case, as the crystal lattice is alchemically turned on, special position overlaps are expected.
         crystal.setSpecialPositionCutoff(0.0);
       } else {
         // If special positions have already been identified, leave checks on.
         logger.info(" Special positions checking will be performed during a lambda simulation.");
       }
     }
   }
 
   private int checkForSpecialPositions(ForceField forceField) {
     // Check for atoms at special positions. These should normally be set to inactive.
     boolean specialPositionsInactive = forceField.getBoolean("SPECIAL_POSITIONS_INACTIVE", true);
     int nSpecial = 0;
     if (specialPositionsInactive) {
       int nSymm = crystal.getNumSymOps();
       if (nSymm > 1) {
         SpaceGroup spaceGroup = crystal.spaceGroup;
         double sp2 = crystal.getSpecialPositionCutoff2();
         double[] mate = new double[3];
         StringBuilder sb = new StringBuilder("\n Atoms at Special Positions set to Inactive:\n");
         for (int i = 0; i < nAtoms; i++) {
           Atom atom = atoms[i];
           double[] xyz = atom.getXYZ(null);
           for (int iSymm = 1; iSymm < nSymm; iSymm++) {
             SymOp symOp = spaceGroup.getSymOp(iSymm);
             crystal.applySymOp(xyz, mate, symOp);
             double dr2 = crystal.image(xyz, mate);
             if (dr2 < sp2) {
               sb.append(
                   format("  %s separation with SymOp %d at %8.6f A.\n", atoms[i], iSymm, sqrt(dr2)));
               atom.setActive(false);
               nSpecial++;
               break;
             }
           }
         }
         if (nSpecial > 0) {
           logger.info(sb.toString());
         }
       }
     }
     return nSpecial;
   }
 
   /**
    * Method to parse the restrain-torsion-cos records.
    *
    * @param properties Configuration properties.
    * @param forceField Force field properties.
    * @return Number of restraint torsions.
    */
   private int configureRestrainTorsions(CompositeConfiguration properties, ForceField forceField) {
     StringBuilder restrainLog = new StringBuilder("\n  Restrain-Torsions");
 
     String[] restrainTorsions = properties.getStringArray("restrain-torsion");
     double torsionUnits = forceField.getDouble("TORSIONUNIT", TorsionType.DEFAULT_TORSION_UNIT);
     List<Torsion> restrainTorsionList = new ArrayList<>(restrainTorsions.length);
     for (String restrainString : restrainTorsions) {
       // Add the key back to the input line.
       restrainString = "restrain-torsion " + restrainString;
       // Split the line on the pound symbol to remove comments.
       String input = restrainString.split("#+")[0];
       // Split the line on whitespace.
       String[] tokens = input.trim().split(" +");
       // Restrain torsion records have a similar form as torsion records.
       // The first four tokens are atom indices instead of atom classes.
       TorsionType torsionType = TorsionType.parse(input, tokens);
       torsionType.torsionUnit = torsionUnits;
 
       // Collect the atom indices.
       int[] atomIndices = torsionType.atomClasses;
       int ai1 = atomIndices[0] - 1;
       int ai2 = atomIndices[1] - 1;
       int ai3 = atomIndices[2] - 1;
       int ai4 = atomIndices[3] - 1;
       Atom a1 = atoms[ai1];
       Atom a2 = atoms[ai2];
       Atom a3 = atoms[ai3];
       Atom a4 = atoms[ai4];
 
       // Collect the bonds between the atoms making up the restrain torsion.
       Bond firstBond = a1.getBond(a2);
       Bond middleBond = a2.getBond(a3);
       Bond lastBond = a3.getBond(a4);
       Torsion torsion = new Torsion(firstBond, middleBond, lastBond);
       torsion.setTorsionType(torsionType);
       restrainTorsionList.add(torsion);
       restrainLog.append("\n   ").append(torsion);
     }
 
     if (!restrainTorsionList.isEmpty()) {
       nRestrainTorsions = restrainTorsionList.size();
       logger.info(restrainLog.toString());
       logger.info(format("  Added %4d torsion restraints.", nRestrainTorsions));
       restrainTorsionTerm = true;
       this.restrainTorsions = restrainTorsionList.toArray(new Torsion[0]);
       restrainTorsionEnergy = 0;
       restrainTorsionTime = 0;
       return restrainTorsionList.size();
     }
 
     return 0;
   }
 
   /**
    * Method to parse the restrain-distance records.
    *
    * @param properties Configuration properties.
    */
   private void configureRestrainDistances(CompositeConfiguration properties) {
 
     String[] bondRestraints = properties.getStringArray("restrain-distance");
     for (String bondRest : bondRestraints) {
       try {
         String[] toks = bondRest.split("\\s+");
         if (toks.length < 2) {
           throw new IllegalArgumentException(
               format(" restrain-distance value %s could not be parsed!", bondRest));
         }
         // Internally, everything starts with 0, but restrain distance starts at 1, so that 1 has to
         // be subtracted
         int at1 = Integer.parseInt(toks[0]) - 1;
         int at2 = Integer.parseInt(toks[1]) - 1;
 
         double forceConst = 100.0;
         double flatBottomRadius = 0;
         Atom a1 = atoms[at1];
         Atom a2 = atoms[at2];
 
         if (toks.length > 2) {
           forceConst = Double.parseDouble(toks[2]);
         }
         double dist;
         switch (toks.length) {
           case 2:
           case 3:
             double[] xyz1 = new double[3];
             xyz1 = a1.getXYZ(xyz1);
             double[] xyz2 = new double[3];
             xyz2 = a2.getXYZ(xyz2);
             // Current distance between restrained atoms
             dist = crystal.minDistOverSymOps(xyz1, xyz2);
             break;
           case 4:
             dist = Double.parseDouble(toks[3]);
             break;
           case 5:
           default:
             double minDist = Double.parseDouble(toks[3]);
             double maxDist = Double.parseDouble(toks[4]);
             dist = 0.5 * (minDist + maxDist);
             flatBottomRadius = 0.5 * Math.abs(maxDist - minDist);
             break;
         }
 
         UnivariateSwitchingFunction switchF;
         double lamStart = RestrainDistance.DEFAULT_RB_LAM_START;
         double lamEnd = RestrainDistance.DEFAULT_RB_LAM_END;
         if (toks.length > 5) {
           int offset = 5;
           if (toks[5].matches("^[01](?:\\.[0-9]*)?")) {
             offset = 6;
             lamStart = Double.parseDouble(toks[5]);
             if (toks[6].matches("^[01](?:\\.[0-9]*)?")) {
               offset = 7;
               lamEnd = Double.parseDouble(toks[6]);
             }
           }
           switchF = UnivariateFunctionFactory.parseUSF(toks, offset);
         } else {
           switchF = new ConstantSwitch();
         }
 
         setRestrainDistance(a1, a2, dist, forceConst, flatBottomRadius, lamStart, lamEnd, switchF);
       } catch (Exception ex) {
         logger.info(format(" Exception in parsing restrain-distance: %s", ex));
       }
     }
   }
 
   /**
    * Configure bonded constraints.
    *
    * @param forceField Force field properties.
    * @return List of constraints.
    */
   private List<Constraint> configureConstraints(ForceField forceField) {
     String constraintStrings = forceField.getString("CONSTRAIN", forceField.getString("RATTLE", null));
     if (constraintStrings == null) {
       return Collections.emptyList();
     }
 
     ArrayList<Constraint> constraints = new ArrayList<>();
     logger.info(format(" Experimental: parsing constraints option %s", constraintStrings));
 
     Set<Bond> numericBonds = new HashSet<>(1);
     Set<Angle> numericAngles = new HashSet<>(1);
 
     // Totally empty constrain option: constrain only X-H bonds. No other options applied.
     if (constraintStrings.isEmpty() || constraintStrings.matches("^\\s*$")) {
       // Assume constraining only X-H bonds (i.e. RIGID-HYDROGEN).
       logger.info(" Constraining X-H bonds.");
       numericBonds = Arrays.stream(bonds).filter(
           (Bond bond) -> bond.getAtom(0).getAtomicNumber() == 1
               || bond.getAtom(1).getAtomicNumber() == 1).collect(Collectors.toSet());
     } else {
       String[] constraintToks = constraintStrings.split("\\s+");
 
       // First, accumulate SETTLE constraints.
       for (String tok : constraintToks) {
         if (tok.equalsIgnoreCase("WATER")) {
           logger.info(" Constraining waters to be rigid based on angle & bonds.");
           // XYZ files, in particular, have waters mislabeled as generic Molecules.
           // First, find any such mislabeled water.
           Stream<MSNode> settleStream = molecularAssembly.getMolecules().stream()
               .filter((MSNode m) -> m.getAtomList().size() == 3).filter((MSNode m) -> {
                 List<Atom> atoms = m.getAtomList();
                 Atom O = null;
                 List<Atom> H = new ArrayList<>(2);
                 for (Atom at : atoms) {
                   int atN = at.getAtomicNumber();
                   if (atN == 8) {
                     O = at;
                   } else if (atN == 1) {
                     H.add(at);
                   }
                 }
                 return O != null && H.size() == 2;
               });
           // Now concatenate the stream with the properly labeled waters.
           settleStream = Stream.concat(settleStream, molecularAssembly.getWater().stream());
           // Map them into new Settle constraints and collect.
           List<SettleConstraint> settleConstraints = settleStream.map(
               (MSNode m) -> m.getAngleList().getFirst()).map(SettleConstraint::settleFactory).toList();
           constraints.addAll(settleConstraints);
 
         } else if (tok.equalsIgnoreCase("DIATOMIC")) {
           logger.severe(" Diatomic distance constraints not yet implemented properly.");
         } else if (tok.equalsIgnoreCase("TRIATOMIC")) {
           logger.severe(
               " Triatomic SETTLE constraints for non-water molecules not yet implemented properly.");
         }
       }
 
       // Second, accumulate bond/angle constraints.
       for (String tok : constraintToks) {
         if (tok.equalsIgnoreCase("BONDS")) {
           numericBonds = new HashSet<>(Arrays.asList(bonds));
         } else if (tok.equalsIgnoreCase("ANGLES")) {
           numericAngles = new HashSet<>(Arrays.asList(angles));
         }
       }
     }
 
     // Remove bonds that are already dealt with via angles.
     for (Angle angle : numericAngles) {
       angle.getBondList().forEach(numericBonds::remove);
     }
 
     // Remove already-constrained angles and bonds (e.g. SETTLE-constrained ones).
     List<Angle> ccmaAngles = numericAngles.stream().filter((Angle ang) -> !ang.isConstrained())
         .collect(Collectors.toList());
     List<Bond> ccmaBonds = numericBonds.stream().filter((Bond bond) -> !bond.isConstrained())
         .collect(Collectors.toList());
 
     CcmaConstraint ccmaConstraint = CcmaConstraint.ccmaFactory(ccmaBonds, ccmaAngles, atoms,
         getMass(), CcmaConstraint.DEFAULT_CCMA_NONZERO_CUTOFF);
     constraints.add(ccmaConstraint);
     logger.info(format(" Added %d constraints.", constraints.size()));
 
     return constraints;
   }
 
   /**
    * Static factory method to create a ForceFieldEnergy, possibly via FFX or OpenMM implementations.
    *
    * @param assembly To create FFE over
    * @return a {@link ffx.potential.ForceFieldEnergy} object.
    */
   public static ForceFieldEnergy energyFactory(MolecularAssembly assembly) {
     return energyFactory(assembly, ParallelTeam.getDefaultThreadCount());
   }
 
   /**
    * Static factory method to create a ForceFieldEnergy, possibly via FFX or OpenMM implementations.
    *
    * @param assembly   To create FFE over
    * @param numThreads Number of threads to use for FFX energy
    * @return A ForceFieldEnergy on some Platform
    */
   @SuppressWarnings("fallthrough")
   public static ForceFieldEnergy energyFactory(MolecularAssembly assembly, int numThreads) {
     ForceField forceField = assembly.getForceField();
     String platformString = toEnumForm(forceField.getString("PLATFORM", "FFX"));
     try {
       Platform platform = Platform.valueOf(platformString);
       switch (platform) {
         case OMM, OMM_REF, OMM_CUDA, OMM_OPENCL:
           try {
             return new OpenMMEnergy(assembly, platform, numThreads);
           } catch (Exception ex) {
             logger.warning(format(" Exception creating OpenMMEnergy: %s", ex));
             ForceFieldEnergy ffxEnergy = assembly.getPotentialEnergy();
             if (ffxEnergy == null) {
               ffxEnergy = new ForceFieldEnergy(assembly, numThreads);
               assembly.setPotential(ffxEnergy);
             }
             return ffxEnergy;
           }
         case OMM_CPU:
           logger.warning(format(" Platform %s not supported; defaulting to FFX", platform));
         default:
           ForceFieldEnergy ffxEnergy = assembly.getPotentialEnergy();
           if (ffxEnergy == null) {
             ffxEnergy = new ForceFieldEnergy(assembly, numThreads);
             assembly.setPotential(ffxEnergy);
           }
           return ffxEnergy;
       }
     } catch (IllegalArgumentException | NullPointerException ex) {
       logger.warning(
           format(" String %s did not match a known energy implementation", platformString));
       ForceFieldEnergy ffxEnergy = assembly.getPotentialEnergy();
       if (ffxEnergy == null) {
         ffxEnergy = new ForceFieldEnergy(assembly, numThreads);
         assembly.setPotential(ffxEnergy);
       }
       return ffxEnergy;
     }
   }
 
   /**
    * Applies constraints to positions
    *
    * @param xPrior Prior coodinates.
    * @param xNew   New coordinates.
    */
   public void applyAllConstraintPositions(double[] xPrior, double[] xNew) {
     applyAllConstraintPositions(xPrior, xNew, DEFAULT_CONSTRAINT_TOLERANCE);
   }
 
   /**
    * Applies constraints to positions
    *
    * @param xPrior Prior coodinates.
    * @param xNew   New coordinates.
    * @param tol    Constraint Tolerance.
    */
   public void applyAllConstraintPositions(double[] xPrior, double[] xNew, double tol) {
     if (xPrior == null) {
       xPrior = Arrays.copyOf(xNew, xNew.length);
     }
     for (Constraint constraint : constraints) {
       constraint.applyConstraintToStep(xPrior, xNew, getMass(), tol);
     }
   }
 
   /**
    * Overwrites current esvSystem if present. Multiple ExtendedSystems is possible but unnecessary;
    * add all ESVs to one system (per FFE, at least).
    *
    * @param system a {@link ffx.potential.extended.ExtendedSystem} object.
    */
   public void attachExtendedSystem(ExtendedSystem system) {
     if (system == null) {
       throw new IllegalArgumentException();
     }
     esvTerm = true;
     esvTermOrig = esvTerm;
     esvSystem = system;
     if (vanderWaalsTerm) {
       if (vanderWaals == null) {
         logger.warning("Null VdW during ESV setup.");
       } else {
         vanderWaals.attachExtendedSystem(system);
       }
     }
     if (multipoleTerm) {
       if (particleMeshEwald == null) {
         logger.warning("Null PME during ESV setup.");
       } else {
         particleMeshEwald.attachExtendedSystem(system);
       }
     }
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Returns true if lambda term is not enabled for this ForceFieldEnergy.
    */
   @Override
   public boolean dEdLZeroAtEnds() {
     // This may actually be true even with softcored atoms.
     // For now, serves the purpose of reporting true when nothing is softcored.
     return !lambdaTerm;
   }
 
   /**
    * Frees up assets associated with this ForceFieldEnergy, such as worker Threads.
    *
    * @return If successful in freeing up assets.
    */
   public boolean destroy() {
     if (destroyed) {
       // This regularly occurs with Repex OST, as multiple OrthogonalSpaceTempering objects wrap a
       // single FFE.
       logger.fine(format(" This ForceFieldEnergy is already destroyed: %s", this));
       return true;
     } else {
       try {
         if (parallelTeam != null) {
           parallelTeam.shutdown();
         }
         if (vanderWaals != null) {
           vanderWaals.destroy();
         }
         if (particleMeshEwald != null) {
           particleMeshEwald.destroy();
         }
         molecularAssembly.finishDestruction();
         destroyed = true;
         return true;
       } catch (Exception ex) {
         logger.warning(format(" Exception in shutting down a ForceFieldEnergy: %s", ex));
         logger.info(Utilities.stackTraceToString(ex));
         return false;
       }
     }
   }
 
   /**
    * energy.
    *
    * @return a double.
    */
   public double energy() {
     return energy(false, false);
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>energy
    */
   public double energy(boolean gradient, boolean print) {
     try {
       totalTime = System.nanoTime();
       nnTime = 0;
       bondTime = 0;
       angleTime = 0;
       stretchBendTime = 0;
       ureyBradleyTime = 0;
       outOfPlaneBendTime = 0;
       torsionTime = 0;
       stretchTorsionTime = 0;
       angleTorsionTime = 0;
       piOrbitalTorsionTime = 0;
       torsionTorsionTime = 0;
       improperTorsionTime = 0;
       vanDerWaalsTime = 0;
       electrostaticTime = 0;
       restrainDistanceTime = 0;
       restrainTorsionTime = 0;
       restrainPositionTime = 0;
       restrainGroupTime = 0;
       ncsTime = 0;
 
       // Zero out the potential energy of each bonded term.
       nnEnergy = 0.0;
       bondEnergy = 0.0;
       angleEnergy = 0.0;
       stretchBendEnergy = 0.0;
       ureyBradleyEnergy = 0.0;
       outOfPlaneBendEnergy = 0.0;
       torsionEnergy = 0.0;
       angleTorsionEnergy = 0.0;
       stretchTorsionEnergy = 0.0;
       piOrbitalTorsionEnergy = 0.0;
       torsionTorsionEnergy = 0.0;
       improperTorsionEnergy = 0.0;
       totalBondedEnergy = 0.0;
 
       // Zero out potential energy of restraint terms
       restrainDistanceEnergy = 0.0;
       restrainTorsionEnergy = 0.0;
       restrainPositionEnergy = 0.0;
       restrainGroupEnergy = 0.0;
       ncsEnergy = 0.0;
 
       // Zero out bond and angle RMSDs.
       bondRMSD = 0.0;
       angleRMSD = 0.0;
 
       // Zero out the potential energy of each non-bonded term.
       vanDerWaalsEnergy = 0.0;
       permanentMultipoleEnergy = 0.0;
       permanentRealSpaceEnergy = 0.0;
       polarizationEnergy = 0.0;
       totalMultipoleEnergy = 0.0;
       totalNonBondedEnergy = 0.0;
 
       // Zero out the solvation energy.
       solvationEnergy = 0.0;
 
       // Zero out the relative solvation energy (sequence optimization)
       relativeSolvationEnergy = 0.0;
       nRelativeSolvations = 0;
 
       esvBias = 0.0;
 
       // Zero out the total potential energy.
       totalEnergy = 0.0;
 
       // Zero out the Cartesian coordinate gradient for each atom.
       //            if (gradient) {
       //                for (int i = 0; i < nAtoms; i++) {
       //                    atoms[i].setXYZGradient(0.0, 0.0, 0.0);
       //                    atoms[i].setLambdaXYZGradient(0.0, 0.0, 0.0);
       //                }
       //            }
 
       // Computed the bonded energy terms in parallel.
       try {
         bondedRegion.setGradient(gradient);
         parallelTeam.execute(bondedRegion);
       } catch (RuntimeException ex) {
         logger.warning("Runtime exception during bonded term calculation.");
         throw ex;
       } catch (Exception ex) {
         logger.info(Utilities.stackTraceToString(ex));
         logger.severe(ex.toString());
       }
 
       if (!lambdaBondedTerms) {
         // Compute restraint terms.
         if (ncsTerm) {
           ncsTime = -System.nanoTime();
           ncsEnergy = ncsRestraint.residual(gradient, print);
           ncsTime += System.nanoTime();
         }
 
         /*
         if (restrainPositionTerm) {
           restrainPositionTime = -System.nanoTime();
           for (RestrainPosition restrainPosition : restrainPositions) {
             restrainPositionEnergy += restrainPosition.residual(gradient);
           }
           restrainPositionTime += System.nanoTime();
         }
         */
 
         if (restrainGroupTerm) {
           restrainGroupTime = -System.nanoTime();
           restrainGroupEnergy = restrainGroups.energy(gradient);
           restrainGroupTime += System.nanoTime();
         }
 
         if (comTerm) {
           comRestraintTime = -System.nanoTime();
           comRestraintEnergy = comRestraint.residual(gradient, print);
           comRestraintTime += System.nanoTime();
         }
 
 
         // Compute the neural network term.
         if (nnTerm) {
           nnTime = -System.nanoTime();
           nnEnergy = aniEnergy.energy(gradient, print);
           nnTime += System.nanoTime();
         }
 
         // Compute non-bonded terms.
         if (vanderWaalsTerm) {
           vanDerWaalsTime = -System.nanoTime();
           vanDerWaalsEnergy = vanderWaals.energy(gradient, print);
           nVanDerWaalInteractions = this.vanderWaals.getInteractions();
           vanDerWaalsTime += System.nanoTime();
         }
 
         if (multipoleTerm) {
           electrostaticTime = -System.nanoTime();
           totalMultipoleEnergy = particleMeshEwald.energy(gradient, print);
           permanentMultipoleEnergy = particleMeshEwald.getPermanentEnergy();
           permanentRealSpaceEnergy = particleMeshEwald.getPermRealEnergy();
           polarizationEnergy = particleMeshEwald.getPolarizationEnergy();
           nPermanentInteractions = particleMeshEwald.getInteractions();
           solvationEnergy = particleMeshEwald.getSolvationEnergy();
           nGKInteractions = particleMeshEwald.getGKInteractions();
           electrostaticTime += System.nanoTime();
         }
       }
 
       if (relativeSolvationTerm) {
         List<Residue> residuesList = molecularAssembly.getResidueList();
         for (Residue residue : residuesList) {
           if (residue instanceof MultiResidue) {
             Atom refAtom = residue.getSideChainAtoms().get(0);
             if (refAtom != null && refAtom.getUse()) {
               // Reasonably confident that it should be -=,
               // as we are trying to penalize residues with strong solvation energy.
               double thisSolvation = relativeSolvation.getSolvationEnergy(residue, false);
               relativeSolvationEnergy -= thisSolvation;
               if (thisSolvation != 0) {
                 nRelativeSolvations++;
               }
             }
           }
         }
       }
 
       totalTime = System.nanoTime() - totalTime;
 
       totalBondedEnergy = nnEnergy + bondEnergy + angleEnergy + stretchBendEnergy + ureyBradleyEnergy
           + outOfPlaneBendEnergy + torsionEnergy + angleTorsionEnergy + stretchTorsionEnergy
           + piOrbitalTorsionEnergy + improperTorsionEnergy + torsionTorsionEnergy
           + ncsEnergy + comRestraintEnergy
           + restrainDistanceEnergy + restrainPositionEnergy + restrainGroupEnergy + restrainTorsionEnergy;
 
       totalNonBondedEnergy = vanDerWaalsEnergy + totalMultipoleEnergy + relativeSolvationEnergy;
       totalEnergy = totalBondedEnergy + totalNonBondedEnergy + solvationEnergy;
       if (esvTerm) {
         esvBias = esvSystem.getBiasEnergy();
         totalEnergy += esvBias;
       }
 
       if (print) {
         StringBuilder sb = new StringBuilder();
         if (gradient) {
           sb.append("\n Computed Potential Energy and Atomic Coordinate Gradients\n");
         } else {
           sb.append("\n Computed Potential Energy\n");
         }
         sb.append(this);
         logger.info(sb.toString());
       }
       return totalEnergy;
     } catch (EnergyException ex) {
       if (printOnFailure) {
         printFailure();
       }
       if (ex.doCauseSevere()) {
         logger.info(Utilities.stackTraceToString(ex));
         logger.log(Level.SEVERE, " Error in calculating energies or gradients", ex);
       } else {
         logger.log(Level.INFO, format(" Exception in energy calculation:\n %s", ex));
       }
       throw ex;
     }
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double energy(double[] x) {
     return energy(x, false);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double energy(double[] x, boolean verbose) {
     assert Arrays.stream(x).allMatch(Double::isFinite);
 
     // Unscale the coordinates.
     unscaleCoordinates(x);
 
     // Set coordinates.
     setCoordinates(x);
 
     double e = this.energy(false, verbose);
 
     // Rescale the coordinates.
     scaleCoordinates(x);
 
     return e;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double energyAndGradient(double[] x, double[] g) {
     return energyAndGradient(x, g, false);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double energyAndGradient(double[] x, double[] g, boolean verbose) {
     assert Arrays.stream(x).allMatch(Double::isFinite);
     // Un-scale the coordinates.
     unscaleCoordinates(x);
     // Set coordinates.
     setCoordinates(x);
     double e = energy(true, verbose);
 
     // Try block already exists inside energy(boolean, boolean), so only
     // need to try-catch fillGradient.
     try {
       fillGradient(g);
 
       // Scale the coordinates and gradients.
       scaleCoordinatesAndGradient(x, g);
 
       if (maxDebugGradient < Double.MAX_VALUE) {
         boolean extremeGrad = Arrays.stream(g)
             .anyMatch((double gi) -> (gi > maxDebugGradient || gi < -maxDebugGradient));
         if (extremeGrad) {
           File origFile = molecularAssembly.getFile();
           String timeString = LocalDateTime.now()
               .format(DateTimeFormatter.ofPattern("yyyy_MM_dd-HH_mm_ss"));
 
           String filename = format("%s-LARGEGRAD-%s.pdb",
               removeExtension(molecularAssembly.getFile().getName()), timeString);
           PotentialsFunctions ef = new PotentialsUtils();
           filename = ef.versionFile(filename);
 
           logger.warning(format(" Excessively large gradient detected; printing snapshot to file %s",
               filename));
           ef.saveAsPDB(molecularAssembly, new File(filename));
           molecularAssembly.setFile(origFile);
         }
       }
       return e;
     } catch (EnergyException ex) {
       if (printOnFailure) {
         printFailure();
       }
       if (ex.doCauseSevere()) {
         logger.info(Utilities.stackTraceToString(ex));
         logger.log(Level.SEVERE, " Error in calculating energies or gradients", ex);
       } else {
         logger.log(Level.INFO, format(" Exception in energy calculation:\n %s", ex));
       }
       throw ex;
     }
   }
 
   /**
    * Save coordinates when an EnergyException is caught.
    */
   private void printFailure() {
     String timeString = LocalDateTime.now()
         .format(DateTimeFormatter.ofPattern("yyyy_MM_dd-HH_mm_ss"));
     File file = molecularAssembly.getFile();
     String ext = "pdb";
     if (isXYZ(file)) {
       ext = "xyz";
     }
     String filename = format("%s-ERROR-%s.%s", removeExtension(file.getName()), timeString, ext);
     PotentialsFunctions ef = new PotentialsUtils();
     filename = ef.versionFile(filename);
     logger.info(format(" Writing on-error snapshot to file %s", filename));
     ef.save(molecularAssembly, new File(filename));
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Returns an array of acceleration values for active atoms.
    */
   @Override
   public double[] getAcceleration(double[] acceleration) {
     int n = getNumberOfVariables();
     if (acceleration == null || acceleration.length < n) {
       acceleration = new double[n];
     }
     int index = 0;
     double[] a = new double[3];
     for (int i = 0; i < nAtoms; i++) {
       if (atoms[i].isActive()) {
         atoms[i].getAcceleration(a);
         acceleration[index++] = a[0];
         acceleration[index++] = a[1];
         acceleration[index++] = a[2];
       }
     }
     return acceleration;
   }
 
   /**
    * Getter for the field <code>angleEnergy</code>.
    *
    * @return a double.
    */
   public double getAngleEnergy() {
     return angleEnergy;
   }
 
   /**
    * Getter for the field <code>angleTorsionEnergy</code>.
    *
    * @return a double.
    */
   public double getAngleTorsionEnergy() {
     return angleTorsionEnergy;
   }
 
   /**
    * Getter for the field <code>angleTorsions</code>.
    *
    * @return an array of {@link ffx.potential.bonded.AngleTorsion} objects.
    */
   public AngleTorsion[] getAngleTorsions() {
     return angleTorsions;
   }
 
   /**
    * Getter for the field <code>angles</code>. Both normal and in-plane angles are returned.
    *
    * @return an array of {@link ffx.potential.bonded.Angle} objects.
    */
   public Angle[] getAngles() {
     return angles;
   }
 
   public String getAngleEnergyString() {
     AngleType angleType = angles[0].angleType;
     String energy;
     if (angleType.angleFunction == AngleType.AngleFunction.SEXTIC) {
       energy = format("""
               k*(d^2 + %.15g*d^3 + %.15g*d^4 + %.15g*d^5 + %.15g*d^6);
               d=%.15g*theta-theta0;
               """,
           angleType.cubic, angleType.quartic, angleType.pentic, angleType.sextic, 180.0 / PI);
     } else {
       energy = format("""
               k*(d^2);
               d=%.15g*theta-theta0;
               """,
           180.0 / PI);
     }
     return energy;
   }
 
   public String getInPlaneAngleEnergyString() {
     AngleType angleType = angles[0].angleType;
     String energy = format("""
             k*(d^2 + %.15g*d^3 + %.15g*d^4 + %.15g*d^5 + %.15g*d^6);
             d=theta-theta0;
             theta = %.15g*pointangle(x1, y1, z1, projx, projy, projz, x3, y3, z3);
             projx = x2-nx*dot;
             projy = y2-ny*dot;
             projz = z2-nz*dot;
             dot = nx*(x2-x3) + ny*(y2-y3) + nz*(z2-z3);
             nx = px/norm;
             ny = py/norm;
             nz = pz/norm;
             norm = sqrt(px*px + py*py + pz*pz);
             px = (d1y*d2z-d1z*d2y);
             py = (d1z*d2x-d1x*d2z);
             pz = (d1x*d2y-d1y*d2x);
             d1x = x1-x4;
             d1y = y1-y4;
             d1z = z1-z4;
             d2x = x3-x4;
             d2y = y3-y4;
             d2z = z3-z4;
             """,
         angleType.cubic, angleType.quartic, angleType.pentic, angleType.sextic, 180.0 / PI);
     return energy;
   }
 
   /**
    * Getter for the field <code>angles</code> with only <code>AngleMode</code> angles.
    *
    * @param angleMode Only angles of this mode will be returned.
    * @return an array of {@link ffx.potential.bonded.Angle} objects.
    */
   public Angle[] getAngles(AngleMode angleMode) {
     if (angles == null || angles.length < 1) {
       return null;
     }
     int nAngles = angles.length;
     List<Angle> angleList = new ArrayList<>();
     // Sort all normal angles from in-plane angles
     for (int i = 0; i < nAngles; i++) {
       if (angles[i].getAngleMode() == angleMode) {
         angleList.add(angles[i]);
       }
     }
     nAngles = angleList.size();
     if (nAngles < 1) {
       return null;
     }
     return angleList.toArray(new Angle[0]);
   }
 
 
   /**
    * Getter for the field <code>nnEnergy</code>.
    *
    * @return a double.
    */
   public double getNeutralNetworkEnergy() {
     return nnEnergy;
   }
 
   /**
    * Getter for the field <code>bondEnergy</code>.
    *
    * @return a double.
    */
   public double getBondEnergy() {
     return bondEnergy;
   }
 
   /**
    * Getter for the field <code>bonds</code>.
    *
    * @return an array of {@link ffx.potential.bonded.Bond} objects.
    */
   public Bond[] getBonds() {
     return bonds;
   }
 
   public String getBondEnergyString() {
     BondType bondType = bonds[0].getBondType();
     String energy;
     if (bondType.bondFunction == BondType.BondFunction.QUARTIC) {
       energy = format("""
               k*(d^2 + %.15g*d^3 + %.15g*d^4);
               d=r-r0;
               """,
           bondType.cubic / OpenMM_NmPerAngstrom,
           bondType.quartic / (OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom));
     } else {
       energy = """
           k*(d^2);
           d=r-r0;
           """;
     }
     return energy;
   }
 
   /**
    * getCavitationEnergy.
    *
    * @return a double.
    */
   public double getCavitationEnergy() {
     return particleMeshEwald.getCavitationEnergy();
   }
 
   /**
    * Returns a copy of the list of constraints this ForceFieldEnergy has.
    *
    * @return Copied list of constraints.
    */
   @Override
   public List<Constraint> getConstraints() {
     return constraints.isEmpty() ? Collections.emptyList() : new ArrayList<>(constraints);
   }
 
   /**
    * Getter for the field <code>coordRestraints</code>.
    *
    * @return a {@link java.util.List} object.
    */
   public List<RestrainPosition> getRestrainPositions() {
     if (restrainPositions == null) {
       return Collections.emptyList();
     }
     return List.of(restrainPositions);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double[] getCoordinates(double[] x) {
     int n = getNumberOfVariables();
     if (x == null || x.length < n) {
       x = new double[n];
     }
     int index = 0;
     for (int i = 0; i < nAtoms; i++) {
       Atom a = atoms[i];
       if (a.isActive()) {
         x[index++] = a.getX();
         x[index++] = a.getY();
         x[index++] = a.getZ();
       }
     }
     return x;
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Getter for the field <code>crystal</code>.
    */
   @Override
   public Crystal getCrystal() {
     return crystal;
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Set the boundary conditions for this calculation.
    */
   @Override
   public void setCrystal(Crystal crystal) {
     setCrystal(crystal, false);
   }
 
   /**
    * Getter for the field <code>cutoffPlusBuffer</code>.
    *
    * @return a double.
    */
   public double getCutoffPlusBuffer() {
     return cutoffPlusBuffer;
   }
 
   /**
    * getDispersionEnergy.
    *
    * @return a double.
    */
   public double getDispersionEnergy() {
     return particleMeshEwald.getDispersionEnergy();
   }
 
   /**
    * getElectrostaticEnergy.
    *
    * @return a double.
    */
   public double getElectrostaticEnergy() {
     return totalMultipoleEnergy;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public STATE getEnergyTermState() {
     return state;
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>This method is for the RESPA integrator only.
    */
   @Override
   public void setEnergyTermState(STATE state) {
     this.state = state;
     switch (state) {
       case FAST:
         nnTerm = nnTermOrig;
         bondTerm = bondTermOrig;
         angleTerm = angleTermOrig;
         stretchBendTerm = stretchBendTermOrig;
         ureyBradleyTerm = ureyBradleyTermOrig;
         outOfPlaneBendTerm = outOfPlaneBendTermOrig;
         torsionTerm = torsionTermOrig;
         stretchTorsionTerm = stretchTorsionTermOrig;
         angleTorsionTerm = angleTorsionTermOrig;
         piOrbitalTorsionTerm = piOrbitalTorsionTermOrig;
         torsionTorsionTerm = torsionTorsionTermOrig;
         improperTorsionTerm = improperTorsionTermOrig;
         restrainDistanceTerm = restrainDistanceTermOrig;
         restrainTorsionTerm = restrainTorsionTermOrig;
         restrainPositionTerm = restrainPositionTermOrig;
         restrainGroupTerm = restrainGroupTermOrig;
         ncsTerm = ncsTermOrig;
         comTerm = comTermOrig;
         vanderWaalsTerm = false;
         multipoleTerm = false;
         polarizationTerm = false;
         generalizedKirkwoodTerm = false;
         esvTerm = false;
         break;
       case SLOW:
         vanderWaalsTerm = vanderWaalsTermOrig;
         multipoleTerm = multipoleTermOrig;
         polarizationTerm = polarizationTermOrig;
         generalizedKirkwoodTerm = generalizedKirkwoodTermOrig;
         esvTerm = esvTermOrig;
         nnTerm = false;
         bondTerm = false;
         angleTerm = false;
         stretchBendTerm = false;
         ureyBradleyTerm = false;
         outOfPlaneBendTerm = false;
         torsionTerm = false;
         stretchTorsionTerm = false;
         angleTorsionTerm = false;
         piOrbitalTorsionTerm = false;
         torsionTorsionTerm = false;
         improperTorsionTerm = false;
         restrainDistanceTerm = false;
         restrainPositionTerm = false;
         restrainGroupTerm = false;
         ncsTerm = false;
         comTerm = false;
         break;
       default:
         nnTerm = nnTermOrig;
         bondTerm = bondTermOrig;
         angleTerm = angleTermOrig;
         stretchBendTerm = stretchBendTermOrig;
         ureyBradleyTerm = ureyBradleyTermOrig;
         outOfPlaneBendTerm = outOfPlaneBendTermOrig;
         torsionTerm = torsionTermOrig;
         stretchTorsionTerm = stretchTorsionTermOrig;
         angleTorsionTerm = angleTorsionTermOrig;
         piOrbitalTorsionTerm = piOrbitalTorsionTermOrig;
         torsionTorsionTerm = torsionTorsionTermOrig;
         improperTorsionTerm = improperTorsionTermOrig;
         restrainDistanceTerm = restrainDistanceTermOrig;
         restrainTorsionTerm = restrainTorsionTermOrig;
         restrainPositionTerm = restrainPositionTermOrig;
         restrainGroupTerm = restrainGroupTermOrig;
         ncsTerm = ncsTermOrig;
         comTermOrig = comTerm;
         vanderWaalsTerm = vanderWaalsTermOrig;
         multipoleTerm = multipoleTermOrig;
         polarizationTerm = polarizationTermOrig;
         generalizedKirkwoodTerm = generalizedKirkwoodTermOrig;
     }
   }
 
   /**
    * getEsvBiasEnergy.
    *
    * @return a double.
    */
   public double getEsvBiasEnergy() {
     return esvBias;
   }
 
   /**
    * getExtendedSystem.
    *
    * @return a {@link ffx.potential.extended.ExtendedSystem} object.
    */
   public ExtendedSystem getExtendedSystem() {
     return esvSystem;
   }
 
   /**
    * getGK.
    *
    * @return a {@link ffx.potential.nonbonded.GeneralizedKirkwood} object.
    */
   public GeneralizedKirkwood getGK() {
     if (particleMeshEwald != null) {
       return particleMeshEwald.getGK();
     } else {
       return null;
     }
   }
 
   /**
    * getGKEnergy.
    *
    * @return a double.
    */
   public double getGKEnergy() {
     return particleMeshEwald.getGKEnergy();
   }
 
   /**
    * getGradient
    *
    * @param g an array of double.
    * @return an array of {@link double} objects.
    */
   public double[] getGradient(double[] g) {
     return fillGradient(g);
   }
 
   /**
    * Getter for the field <code>improperTorsionEnergy</code>.
    *
    * @return a double.
    */
   public double getImproperTorsionEnergy() {
     return improperTorsionEnergy;
   }
 
   /**
    * Getter for the field <code>improperTorsions</code>.
    *
    * @return an array of {@link ffx.potential.bonded.ImproperTorsion} objects.
    */
   public ImproperTorsion[] getImproperTorsions() {
     return improperTorsions;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double getLambda() {
     return lambda;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void setLambda(double lambda) {
     if (lambdaTerm) {
       if (lambda <= 1.0 && lambda >= 0.0) {
         this.lambda = lambda;
         if (vanderWaalsTerm) {
           vanderWaals.setLambda(lambda);
         }
         if (multipoleTerm) {
           particleMeshEwald.setLambda(lambda);
         }
 
         /*
         if (restrainPositionTerm && nRestrainPositions > 0) {
           for (RestrainPosition restrainPosition : restrainPositions) {
             restrainPosition.setLambda(lambda);
           }
         } */
 
         if (restrainDistanceTerm && nRestrainDistances > 0) {
           for (RestrainDistance restrainDistance : restrainDistances) {
             restrainDistance.setLambda(lambda);
           }
         }
         if (restrainTorsionTerm && nRestrainTorsions > 0) {
           for (Torsion restrainTorsion : restrainTorsions) {
             restrainTorsion.setLambda(lambda);
           }
         }
 
         if (ncsTerm && ncsRestraint != null) {
           ncsRestraint.setLambda(lambda);
         }
         if (comTerm && comRestraint != null) {
           comRestraint.setLambda(lambda);
         }
         if (lambdaTorsions) {
           for (int i = 0; i < nTorsions; i++) {
             torsions[i].setLambda(lambda);
           }
           for (int i = 0; i < nPiOrbitalTorsions; i++) {
             piOrbitalTorsions[i].setLambda(lambda);
           }
           for (int i = 0; i < nTorsionTorsions; i++) {
             torsionTorsions[i].setLambda(lambda);
           }
         }
       } else {
         String message = format("Lambda value %8.3f is not in the range [0..1].", lambda);
         logger.warning(message);
       }
     } else {
       logger.fine(" Attempting to set a lambda value on a ForceFieldEnergy with lambdaterm false.");
     }
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double[] getMass() {
     int n = getNumberOfVariables();
     double[] mass = new double[n];
     int index = 0;
     for (int i = 0; i < nAtoms; i++) {
       Atom a = atoms[i];
       if (a.isActive()) {
         double m = a.getMass();
         mass[index++] = m;
         mass[index++] = m;
         mass[index++] = m;
       }
     }
     return mass;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public int getNumberOfVariables() {
     int nActive = 0;
     for (int i = 0; i < nAtoms; i++) {
       if (atoms[i].isActive()) {
         nActive++;
       }
     }
     return nActive * 3;
   }
 
   /**
    * getNumberofAngleTorsions.
    *
    * @return a int.
    */
   public int getNumberofAngleTorsions() {
     return nAngleTorsions;
   }
 
   /**
    * getNumberofAngles.
    *
    * @return a int.
    */
   public int getNumberofAngles() {
     return nAngles;
   }
 
   /**
    * getNumberofBonds.
    *
    * @return a int.
    */
   public int getNumberofBonds() {
     return nBonds;
   }
 
   /**
    * getNumberofImproperTorsions.
    *
    * @return a int.
    */
   public int getNumberofImproperTorsions() {
     return nImproperTorsions;
   }
 
   /**
    * getNumberofOutOfPlaneBends.
    *
    * @return a int.
    */
   public int getNumberofOutOfPlaneBends() {
     return nOutOfPlaneBends;
   }
 
   /**
    * getNumberofPiOrbitalTorsions.
    *
    * @return a int.
    */
   public int getNumberofPiOrbitalTorsions() {
     return nPiOrbitalTorsions;
   }
 
   /**
    * getNumberofStretchBends.
    *
    * @return a int.
    */
   public int getNumberofStretchBends() {
     return nStretchBends;
   }
 
   /**
    * getNumberofStretchTorsions.
    *
    * @return a int.
    */
   public int getNumberofStretchTorsions() {
     return nStretchTorsions;
   }
 
   /**
    * getNumberofTorsionTorsions.
    *
    * @return a int.
    */
   public int getNumberofTorsionTorsions() {
     return nTorsionTorsions;
   }
 
   /**
    * getNumberofTorsions.
    *
    * @return a int.
    */
   public int getNumberofTorsions() {
     return nTorsions;
   }
 
   /**
    * getNumberofUreyBradleys.
    *
    * @return a int.
    */
   public int getNumberofUreyBradleys() {
     return nUreyBradleys;
   }
 
   /**
    * Getter for the field <code>outOfPlaneBendEnergy</code>.
    *
    * @return a double.
    */
   public double getOutOfPlaneBendEnergy() {
     return outOfPlaneBendEnergy;
   }
 
   /**
    * Getter for the field <code>outOfPlaneBends</code>.
    *
    * @return an array of {@link ffx.potential.bonded.OutOfPlaneBend} objects.
    */
   public OutOfPlaneBend[] getOutOfPlaneBends() {
     return outOfPlaneBends;
   }
 
   public String getOutOfPlaneEnergyString() {
     OutOfPlaneBendType outOfPlaneBendType = outOfPlaneBends[0].outOfPlaneBendType;
     String energy = format(""" 
             k*(theta^2 + %.15g*theta^3 + %.15g*theta^4 + %.15g*theta^5 + %.15g*theta^6);
             theta = %.15g*pointangle(x2, y2, z2, x4, y4, z4, projx, projy, projz);
             projx = x2-nx*dot;
             projy = y2-ny*dot;
             projz = z2-nz*dot;
             dot = nx*(x2-x3) + ny*(y2-y3) + nz*(z2-z3);
             nx = px/norm;
             ny = py/norm;
             nz = pz/norm;
             norm = sqrt(px*px + py*py + pz*pz);
             px = (d1y*d2z-d1z*d2y);
             py = (d1z*d2x-d1x*d2z);
             pz = (d1x*d2y-d1y*d2x);
             d1x = x1-x4;
             d1y = y1-y4;
             d1z = z1-z4;
             d2x = x3-x4;
             d2y = y3-y4;
             d2z = z3-z4
             """,
         outOfPlaneBendType.cubic, outOfPlaneBendType.quartic,
         outOfPlaneBendType.pentic, outOfPlaneBendType.sextic, 180.0 / PI);
     return energy;
   }
 
   /**
    * getPDBHeaderString
    *
    * @return a {@link java.lang.String} object.
    */
   public String getPDBHeaderString() {
     energy(false, false);
     StringBuilder sb = new StringBuilder();
     sb.append("REMARK   3  CALCULATED POTENTIAL ENERGY\n");
     if (nnTerm) {
       sb.append(
           format("REMARK   3   %s %g (%d)\n", "NEUTRAL NETWORK            : ", nnEnergy, nAtoms));
     }
     if (bondTerm) {
       sb.append(
           format("REMARK   3   %s %g (%d)\n", "BOND STRETCHING            : ", bondEnergy, nBonds));
       sb.append(format("REMARK   3   %s %g\n", "BOND RMSD                  : ", bondRMSD));
     }
     if (angleTerm) {
       sb.append(format("REMARK   3   %s %g (%d)\n", "ANGLE BENDING              : ", angleEnergy,
           nAngles));
       sb.append(format("REMARK   3   %s %g\n", "ANGLE RMSD                 : ", angleRMSD));
     }
     if (stretchBendTerm) {
       sb.append(
           format("REMARK   3   %s %g (%d)\n", "STRETCH-BEND               : ", stretchBendEnergy,
               nStretchBends));
     }
     if (ureyBradleyTerm) {
       sb.append(
           format("REMARK   3   %s %g (%d)\n", "UREY-BRADLEY               : ", ureyBradleyEnergy,
               nUreyBradleys));
     }
     if (outOfPlaneBendTerm) {
       sb.append(
           format("REMARK   3   %s %g (%d)\n", "OUT-OF-PLANE BEND          : ", outOfPlaneBendEnergy,
               nOutOfPlaneBends));
     }
     if (torsionTerm) {
       sb.append(format("REMARK   3   %s %g (%d)\n", "TORSIONAL ANGLE            : ", torsionEnergy,
           nTorsions));
     }
     if (piOrbitalTorsionTerm) {
       sb.append(format("REMARK   3   %s %g (%d)\n", "PI-ORBITAL TORSION         : ",
           piOrbitalTorsionEnergy, nPiOrbitalTorsions));
     }
     if (torsionTorsionTerm) {
       sb.append(
           format("REMARK   3   %s %g (%d)\n", "TORSION-TORSION            : ", torsionTorsionEnergy,
               nTorsionTorsions));
     }
     if (improperTorsionTerm) {
       sb.append(
           format("REMARK   3   %s %g (%d)\n", "IMPROPER TORSION           : ", improperTorsionEnergy,
               nImproperTorsions));
     }
     if (restrainDistanceTerm) {
       sb.append(format("REMARK   3   %s %g (%d)\n", "RESTRAINT BOND STRETCHING            : ",
           restrainDistanceEnergy, nRestrainDistances));
     }
 
     if (ncsTerm) {
       sb.append(
           format("REMARK   3   %s %g (%d)\n", "NCS RESTRAINT              : ", ncsEnergy, nAtoms));
     }
 
     if (restrainPositionTerm && nRestrainPositions > 0) {
       int nRests = 0;
       for (RestrainPosition restrainPosition : restrainPositions) {
         nRests += restrainPosition.getNumAtoms();
       }
       sb.append(format("REMARK   3   %s %g (%d)\n", "COORDINATE RESTRAINTS      : ", restrainPositionEnergy,
           nRests));
     }
 
     if (comTerm) {
       sb.append(
           format("REMARK   3   %s %g (%d)\n", "COM RESTRAINT              : ", comRestraintEnergy,
               nAtoms));
     }
 
     if (vanderWaalsTerm) {
       sb.append(
           format("REMARK   3   %s %g (%d)\n", "VAN DER WAALS              : ", vanDerWaalsEnergy,
               nVanDerWaalInteractions));
     }
     if (multipoleTerm) {
       sb.append(format("REMARK   3   %s %g (%d)\n", "ATOMIC MULTIPOLES          : ",
           permanentMultipoleEnergy, nPermanentInteractions));
     }
     if (polarizationTerm) {
       sb.append(format("REMARK   3   %s %g (%d)\n", "POLARIZATION               : ",
           polarizationEnergy, nPermanentInteractions));
     }
     sb.append(format("REMARK   3   %s %g\n", "TOTAL POTENTIAL (KCAL/MOL) : ", totalEnergy));
     int nsymm = crystal.getUnitCell().spaceGroup.getNumberOfSymOps();
     if (nsymm > 1) {
       sb.append(format("REMARK   3   %s %g\n", "UNIT CELL POTENTIAL        : ", totalEnergy * nsymm));
     }
     if (crystal.getUnitCell() != crystal) {
       nsymm = crystal.spaceGroup.getNumberOfSymOps();
       if (nsymm > 1) {
         sb.append(format("REMARK   3   %s %g\n", "REPLICATES CELL POTENTIAL  : ", totalEnergy * nsymm));
       }
     }
     sb.append("REMARK   3\n");
 
     return sb.toString();
   }
 
   /**
    * Getter for the field <code>parallelTeam</code>.
    *
    * @return a {@link edu.rit.pj.ParallelTeam} object.
    */
   public ParallelTeam getParallelTeam() {
     return parallelTeam;
   }
 
   /**
    * getPermanentInteractions.
    *
    * @return a int.
    */
   public int getPermanentInteractions() {
     return nPermanentInteractions;
   }
 
   /**
    * Getter for the field <code>permanentMultipoleEnergy</code>.
    *
    * @return a double.
    */
   public double getPermanentMultipoleEnergy() {
     return permanentMultipoleEnergy;
   }
 
   /**
    * Getter for the field <code>permanentRealSpaceEnergy</code>.
    *
    * @return a double.
    */
   public double getPermanentRealSpaceEnergy() {
     return permanentRealSpaceEnergy;
   }
 
   /**
    * getPermanentReciprocalMpoleEnergy.
    *
    * @return a double.
    */
   public double getPermanentReciprocalMpoleEnergy() {
     return particleMeshEwald.getPermRecipEnergy();
   }
 
   /**
    * getPermanentReciprocalSelfEnergy.
    *
    * @return a double.
    */
   public double getPermanentReciprocalSelfEnergy() {
     return particleMeshEwald.getPermSelfEnergy();
   }
 
   /**
    * Getter for the field <code>piOrbitalTorsionEnergy</code>.
    *
    * @return a double.
    */
   public double getPiOrbitalTorsionEnergy() {
     return piOrbitalTorsionEnergy;
   }
 
   /**
    * Getter for the field <code>piOrbitalTorsions</code>.
    *
    * @return an array of {@link ffx.potential.bonded.PiOrbitalTorsion} objects.
    */
   public PiOrbitalTorsion[] getPiOrbitalTorsions() {
     return piOrbitalTorsions;
   }
 
   public String getPiOrbitalTorsionEnergyString() {
     String energy = """
         2*k*sin(phi)^2;
         phi = pointdihedral(x3+c1x, y3+c1y, z3+c1z, x3, y3, z3, x4, y4, z4, x4+c2x, y4+c2y, z4+c2z);
         c1x = (d14y*d24z-d14z*d24y);
         c1y = (d14z*d24x-d14x*d24z);
         c1z = (d14x*d24y-d14y*d24x);
         c2x = (d53y*d63z-d53z*d63y);
         c2y = (d53z*d63x-d53x*d63z);
         c2z = (d53x*d63y-d53y*d63x);
         d14x = x1-x4;
         d14y = y1-y4;
         d14z = z1-z4;
         d24x = x2-x4;
         d24y = y2-y4;
         d24z = z2-z4;
         d53x = x5-x3;
         d53y = y5-y3;
         d53z = z5-z3;
         d63x = x6-x3;
         d63y = y6-y3;
         d63z = z6-z3;
         """;
     return energy;
   }
 
   /**
    * Gets the Platform associated with this force field energy. For the reference platform, always
    * returns FFX.
    *
    * @return A Platform.
    */
   public Platform getPlatform() {
     return platform;
   }
 
   /**
    * getPmeNode.
    *
    * @return a {@link ParticleMeshEwald} object.
    */
   public ParticleMeshEwald getPmeNode() {
     return particleMeshEwald;
   }
 
   /**
    * Getter for the field <code>polarizationEnergy</code>.
    *
    * @return a double.
    */
   public double getPolarizationEnergy() {
     return polarizationEnergy;
   }
 
 
   /**
    * {@inheritDoc}
    *
    * <p>Returns an array of previous acceleration values for active atoms.
    */
   @Override
   public double[] getPreviousAcceleration(double[] previousAcceleration) {
     int n = getNumberOfVariables();
     if (previousAcceleration == null || previousAcceleration.length < n) {
       previousAcceleration = new double[n];
     }
     int index = 0;
     double[] a = new double[3];
     for (int i = 0; i < nAtoms; i++) {
       if (atoms[i].isActive()) {
         atoms[i].getPreviousAcceleration(a);
         previousAcceleration[index++] = a[0];
         previousAcceleration[index++] = a[1];
         previousAcceleration[index++] = a[2];
       }
     }
     return previousAcceleration;
   }
 
   /**
    * Getter for the field <code>relativeSolvationEnergy</code>.
    *
    * @return a double.
    */
   public double getRelativeSolvationEnergy() {
     return relativeSolvationEnergy;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double[] getScaling() {
     return optimizationScaling;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void setScaling(double[] scaling) {
     optimizationScaling = scaling;
   }
 
   /**
    * Getter for the field <code>solvationEnergy</code>.
    *
    * @return a double.
    */
   public double getSolvationEnergy() {
     return solvationEnergy;
   }
 
   /**
    * getSolvationInteractions.
    *
    * @return a int.
    */
   public int getSolvationInteractions() {
     return nGKInteractions;
   }
 
   /**
    * getStrenchBendEnergy.
    *
    * @return a double.
    */
   public double getStrenchBendEnergy() {
     return stretchBendEnergy;
   }
 
   /**
    * Getter for the field <code>stretchBends</code>.
    *
    * @return an array of {@link ffx.potential.bonded.StretchBend} objects.
    */
   public StretchBend[] getStretchBends() {
     return stretchBends;
   }
 
   public String getStretchBendEnergyString() {
     String energy = format("(k1*(distance(p1,p2)-r12) + k2*(distance(p2,p3)-r23))*(%.15g*(angle(p1,p2,p3)-theta0))", 180.0 / PI);
     return energy;
   }
 
   /**
    * Getter for the field <code>stretchTorsionEnergy</code>.
    *
    * @return a double.
    */
   public double getStretchTorsionEnergy() {
     return stretchTorsionEnergy;
   }
 
   /**
    * Getter for the field <code>stretchTorsions</code>.
    *
    * @return an array of {@link ffx.potential.bonded.StretchTorsion} objects.
    */
   public StretchTorsion[] getStretchTorsions() {
     return stretchTorsions;
   }
 
   /**
    * Getter for the field <code>torsionEnergy</code>.
    *
    * @return a double.
    */
   public double getTorsionEnergy() {
     return torsionEnergy;
   }
 
   /**
    * Getter for the field <code>torsionTorsionEnergy</code>.
    *
    * @return a double.
    */
   public double getTorsionTorsionEnergy() {
     return torsionTorsionEnergy;
   }
 
   /**
    * Getter for the field <code>torsionTorsions</code>.
    *
    * @return an array of {@link ffx.potential.bonded.TorsionTorsion} objects.
    */
   public TorsionTorsion[] getTorsionTorsions() {
     return torsionTorsions;
   }
 
   /**
    * Getter for the field <code>torsions</code>.
    *
    * @return an array of {@link ffx.potential.bonded.Torsion} objects.
    */
   public Torsion[] getTorsions() {
     return torsions;
   }
 
   /**
    * getTotalElectrostaticEnergy.
    *
    * @return a double.
    */
   public double getTotalElectrostaticEnergy() {
     return totalMultipoleEnergy + solvationEnergy;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double getTotalEnergy() {
     return totalEnergy;
   }
 
   /**
    * Getter for the field <code>ureyBradleyEnergy</code>.
    *
    * @return a double.
    */
   public double getUreyBradleyEnergy() {
     return ureyBradleyEnergy;
   }
 
   /**
    * Getter for the field <code>ureyBradleys</code>.
    *
    * @return an array of {@link ffx.potential.bonded.UreyBradley} objects.
    */
   public UreyBradley[] getUreyBradleys() {
     return ureyBradleys;
   }
 
   /**
    * Getter for the field <code>vanDerWaalsEnergy</code>.
    *
    * @return a double.
    */
   public double getVanDerWaalsEnergy() {
     return vanDerWaalsEnergy;
   }
 
   /**
    * getVanDerWaalsInteractions.
    *
    * @return a int.
    */
   public int getVanDerWaalsInteractions() {
     return nVanDerWaalInteractions;
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Return a reference to each variables type.
    */
   @Override
   public VARIABLE_TYPE[] getVariableTypes() {
     int n = getNumberOfVariables();
     VARIABLE_TYPE[] type = new VARIABLE_TYPE[n];
     int i = 0;
     for (int j = 0; j < nAtoms; j++) {
       if (atoms[j].isActive()) {
         type[i++] = VARIABLE_TYPE.X;
         type[i++] = VARIABLE_TYPE.Y;
         type[i++] = VARIABLE_TYPE.Z;
       }
     }
     return type;
   }
 
   /**
    * getVdwNode.
    *
    * @return a {@link ffx.potential.nonbonded.VanDerWaals} object.
    */
   public VanDerWaals getVdwNode() {
     return vanderWaals;
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Returns an array of velocity values for active atoms.
    */
   @Override
   public double[] getVelocity(double[] velocity) {
     int n = getNumberOfVariables();
     if (velocity == null || velocity.length < n) {
       velocity = new double[n];
     }
     int index = 0;
     double[] v = new double[3];
     for (int i = 0; i < nAtoms; i++) {
       Atom a = atoms[i];
       if (a.isActive()) {
         a.getVelocity(v);
         velocity[index++] = v[0];
         velocity[index++] = v[1];
         velocity[index++] = v[2];
       }
     }
     return velocity;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double getd2EdL2() {
     double d2EdLambda2 = 0.0;
     if (!lambdaBondedTerms) {
       if (vanderWaalsTerm) {
         d2EdLambda2 = vanderWaals.getd2EdL2();
       }
       if (multipoleTerm) {
         d2EdLambda2 += particleMeshEwald.getd2EdL2();
       }
       /*
       if (restrainPositionTerm && nRestrainPositions > 0) {
         for (RestrainPosition restrainPosition : restrainPositions) {
           d2EdLambda2 += restrainPosition.getd2EdL2();
         }
       }
       */
       if (restrainDistanceTerm && nRestrainDistances > 0) {
         for (int i = 0; i < nRestrainDistances; i++) {
           d2EdLambda2 += restrainDistances[i].getd2EdL2();
         }
       }
       if (ncsTerm && ncsRestraint != null) {
         d2EdLambda2 += ncsRestraint.getd2EdL2();
       }
       if (comTerm && comRestraint != null) {
         d2EdLambda2 += comRestraint.getd2EdL2();
       }
       if (lambdaTorsions) {
         for (int i = 0; i < nTorsions; i++) {
           d2EdLambda2 += torsions[i].getd2EdL2();
         }
         for (int i = 0; i < nPiOrbitalTorsions; i++) {
           d2EdLambda2 += piOrbitalTorsions[i].getd2EdL2();
         }
         for (int i = 0; i < nTorsionTorsions; i++) {
           d2EdLambda2 += torsionTorsions[i].getd2EdL2();
         }
       }
     }
     return d2EdLambda2;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double getdEdL() {
     double dEdLambda = 0.0;
     if (!lambdaBondedTerms) {
       if (vanderWaalsTerm) {
         dEdLambda = vanderWaals.getdEdL();
       }
       if (multipoleTerm) {
         dEdLambda += particleMeshEwald.getdEdL();
       }
       if (restrainDistanceTerm && nRestrainDistances > 0) {
         for (int i = 0; i < nRestrainDistances; i++) {
           dEdLambda += restrainDistances[i].getdEdL();
         }
       }
       /*
       if (restrainPositionTerm && nRestrainPositions > 0) {
         for (RestrainPosition restrainPosition : restrainPositions) {
           dEdLambda += restrainPosition.getdEdL();
         }
       }
       */
       if (ncsTerm && ncsRestraint != null) {
         dEdLambda += ncsRestraint.getdEdL();
       }
       if (comTerm && comRestraint != null) {
         dEdLambda += comRestraint.getdEdL();
       }
       if (lambdaTorsions) {
         for (int i = 0; i < nTorsions; i++) {
           dEdLambda += torsions[i].getdEdL();
         }
         for (int i = 0; i < nPiOrbitalTorsions; i++) {
           dEdLambda += piOrbitalTorsions[i].getdEdL();
         }
         for (int i = 0; i < nTorsionTorsions; i++) {
           dEdLambda += torsionTorsions[i].getdEdL();
         }
       }
     }
     return dEdLambda;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void getdEdXdL(double[] gradients) {
     if (!lambdaBondedTerms) {
       if (vanderWaalsTerm) {
         vanderWaals.getdEdXdL(gradients);
       }
       if (multipoleTerm) {
         particleMeshEwald.getdEdXdL(gradients);
       }
       if (restrainDistanceTerm && nRestrainDistances > 0) {
         for (int i = 0; i < nRestrainDistances; i++) {
           restrainDistances[i].getdEdXdL(gradients);
         }
       }
       /*
       if (restrainPositionTerm && nRestrainPositions > 0) {
         for (RestrainPosition restrainPosition : restrainPositions) {
           restrainPosition.getdEdXdL(gradients);
         }
       }
       */
       if (ncsTerm && ncsRestraint != null) {
         ncsRestraint.getdEdXdL(gradients);
       }
       if (comTerm && comRestraint != null) {
         comRestraint.getdEdXdL(gradients);
       }
       if (lambdaTorsions) {
         double[] grad = new double[3];
         int index = 0;
         for (int i = 0; i < nAtoms; i++) {
           Atom a = atoms[i];
           if (a.isActive()) {
             a.getLambdaXYZGradient(grad);
             gradients[index++] += grad[0];
             gradients[index++] += grad[1];
             gradients[index++] += grad[2];
           }
         }
       }
     }
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>The acceleration array should only contain acceleration data for active atoms.
    */
   @Override
   public void setAcceleration(double[] acceleration) {
     if (acceleration == null) {
       return;
     }
     int index = 0;
     double[] accel = new double[3];
     for (int i = 0; i < nAtoms; i++) {
       if (atoms[i].isActive()) {
         accel[0] = acceleration[index++];
         accel[1] = acceleration[index++];
         accel[2] = acceleration[index++];
         atoms[i].setAcceleration(accel);
       }
     }
   }
 
   /**
    * The coordinate array should only contain active atoms.
    *
    * @param coords an array of {@link double} objects.
    */
   public void setCoordinates(double[] coords) {
     if (coords == null) {
       return;
     }
     int index = 0;
     for (int i = 0; i < nAtoms; i++) {
       Atom a = atoms[i];
       if (a.isActive()) {
         double x = coords[index++];
         double y = coords[index++];
         double z = coords[index++];
         a.moveTo(x, y, z);
       }
     }
   }
 
   /**
    * Set the boundary conditions for this calculation.
    *
    * @param crystal             Crystal to set.
    * @param checkReplicatesCell Check if a replicates cell must be created.
    */
   public void setCrystal(Crystal crystal, boolean checkReplicatesCell) {
     if (checkReplicatesCell) {
       this.crystal = ReplicatesCrystal.replicatesCrystalFactory(crystal.getUnitCell(), cutOff2);
     } else {
       this.crystal = crystal;
     }
     /*
      Update VanDerWaals first, in case the NeighborList needs to be
      re-allocated to include a larger number of replicated cells.
     */
     if (vanderWaalsTerm) {
       vanderWaals.setCrystal(this.crystal);
     }
     if (multipoleTerm) {
       particleMeshEwald.setCrystal(this.crystal);
     }
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>The previousAcceleration array should only contain previous acceleration data for active
    * atoms.
    */
   @Override
   public void setPreviousAcceleration(double[] previousAcceleration) {
     if (previousAcceleration == null) {
       return;
     }
     int index = 0;
     double[] prev = new double[3];
     for (int i = 0; i < nAtoms; i++) {
       if (atoms[i].isActive()) {
         prev[0] = previousAcceleration[index++];
         prev[1] = previousAcceleration[index++];
         prev[2] = previousAcceleration[index++];
         atoms[i].setPreviousAcceleration(prev);
       }
     }
   }
 
   /**
    * Sets the printOnFailure flag; if override is true, over-rides any existing property. Essentially
    * sets the default value of printOnFailure for an algorithm. For example, rotamer optimization
    * will generally run into force field issues in the normal course of execution as it tries
    * unphysical self and pair configurations, so the algorithm should not print out a large number of
    * error PDBs.
    *
    * @param onFail   To set
    * @param override Override properties
    */
   public void setPrintOnFailure(boolean onFail, boolean override) {
     if (override) {
       // Ignore any pre-existing value
       printOnFailure = onFail;
     } else {
       try {
         molecularAssembly.getForceField().getBoolean("PRINT_ON_FAILURE");
         /*
          If the call was successful, the property was explicitly set
          somewhere and should be kept. If an exception was thrown, the
          property was never set explicitly, so over-write.
         */
       } catch (Exception ex) {
         printOnFailure = onFail;
       }
     }
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>The velocity array should only contain velocity data for active atoms.
    */
   @Override
   public void setVelocity(double[] velocity) {
     if (velocity == null) {
       return;
     }
     int index = 0;
     double[] vel = new double[3];
     for (int i = 0; i < nAtoms; i++) {
       if (atoms[i].isActive()) {
         vel[0] = velocity[index++];
         vel[1] = velocity[index++];
         vel[2] = velocity[index++];
         atoms[i].setVelocity(vel);
       }
     }
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public String toString() {
     StringBuilder sb = new StringBuilder();
     if (bondTerm && nBonds > 0) {
       sb.append(format("  %s %20.8f %12d %12.3f (%8.5f)\n", "Bond Stretching   ", bondEnergy, nBonds,
           bondTime * toSeconds, bondRMSD));
     }
     if (angleTerm && nAngles > 0) {
       sb.append(
           format("  %s %20.8f %12d %12.3f (%8.5f)\n", "Angle Bending     ", angleEnergy, nAngles,
               angleTime * toSeconds, angleRMSD));
     }
     if (stretchBendTerm && nStretchBends > 0) {
       sb.append(
           format("  %s %20.8f %12d %12.3f\n", "Stretch-Bend      ", stretchBendEnergy, nStretchBends,
               stretchBendTime * toSeconds));
     }
     if (ureyBradleyTerm && nUreyBradleys > 0) {
       sb.append(
           format("  %s %20.8f %12d %12.3f\n", "Urey-Bradley      ", ureyBradleyEnergy, nUreyBradleys,
               ureyBradleyTime * toSeconds));
     }
     if (outOfPlaneBendTerm && nOutOfPlaneBends > 0) {
       sb.append(format("  %s %20.8f %12d %12.3f\n", "Out-of-Plane Bend ", outOfPlaneBendEnergy,
           nOutOfPlaneBends, outOfPlaneBendTime * toSeconds));
     }
     if (torsionTerm && nTorsions > 0) {
       sb.append(format("  %s %20.8f %12d %12.3f\n", "Torsional Angle   ", torsionEnergy, nTorsions,
           torsionTime * toSeconds));
     }
     if (piOrbitalTorsionTerm && nPiOrbitalTorsions > 0) {
       sb.append(format("  %s %20.8f %12d %12.3f\n", "Pi-Orbital Torsion", piOrbitalTorsionEnergy,
           nPiOrbitalTorsions, piOrbitalTorsionTime * toSeconds));
     }
     if (stretchTorsionTerm && nStretchTorsions > 0) {
       sb.append(format("  %s %20.8f %12d %12.3f\n", "Stretch-Torsion   ", stretchTorsionEnergy,
           nStretchTorsions, stretchTorsionTime * toSeconds));
     }
     if (angleTorsionTerm && nAngleTorsions > 0) {
       sb.append(format("  %s %20.8f %12d %12.3f\n", "Angle-Torsion     ", angleTorsionEnergy,
           nAngleTorsions, angleTorsionTime * toSeconds));
     }
     if (torsionTorsionTerm && nTorsionTorsions > 0) {
       sb.append(format("  %s %20.8f %12d %12.3f\n", "Torsion-Torsion   ", torsionTorsionEnergy,
           nTorsionTorsions, torsionTorsionTime * toSeconds));
     }
     if (improperTorsionTerm && nImproperTorsions > 0) {
       sb.append(format("  %s %20.8f %12d %12.3f\n", "Improper Torsion  ", improperTorsionEnergy,
           nImproperTorsions, improperTorsionTime * toSeconds));
     }
     if (restrainDistanceTerm && nRestrainDistances > 0) {
       sb.append(format("  %s %20.8f %12d %12.3f\n", "Restrain Distance ", restrainDistanceEnergy,
           nRestrainDistances, restrainDistanceTime * toSeconds));
     }
     if (restrainTorsionTerm && nRestrainTorsions > 0) {
       sb.append(format("  %s %20.8f %12d %12.3f\n", "Restrain Torsion  ", restrainTorsionEnergy, nRestrainTorsions,
           restrainTorsionTime * toSeconds));
     }
     if (restrainPositionTerm && nRestrainPositions > 0) {
       int nRestrainPositionAtoms = 0;
       for (RestrainPosition restrainPosition : restrainPositions) {
         nRestrainPositionAtoms += restrainPosition.getNumAtoms();
       }
       sb.append(format("  %s %20.8f %12d %12.3f\n", "Restrain Position ", restrainPositionEnergy, nRestrainPositionAtoms,
           restrainPositionTime * toSeconds));
     }
     if (restrainGroupTerm && nRestrainGroups > 0) {
       sb.append(format("  %s %20.8f %12d %12.3f\n", "Restrain Groups   ", restrainGroupEnergy,
           nRestrainGroups, restrainGroupTime * toSeconds));
     }
     if (ncsTerm) {
       sb.append(format("  %s %20.8f %12d %12.3f\n", "NCS Restraint     ", ncsEnergy, nAtoms,
           ncsTime * toSeconds));
     }
     if (comTerm) {
       sb.append(format("  %s %20.8f %12d %12.3f\n", "COM Restraint     ", comRestraintEnergy, nAtoms,
           comRestraintTime * toSeconds));
     }
     if (vanderWaalsTerm && nVanDerWaalInteractions > 0) {
       sb.append(format("  %s %20.8f %12d %12.3f\n", "Van der Waals     ", vanDerWaalsEnergy,
           nVanDerWaalInteractions, vanDerWaalsTime * toSeconds));
     }
     if (multipoleTerm && nPermanentInteractions > 0) {
       if (polarizationTerm) {
         sb.append(format("  %s %20.8f %12d\n", "Atomic Multipoles ", permanentMultipoleEnergy,
             nPermanentInteractions));
       } else {
         if (elecForm == ELEC_FORM.FIXED_CHARGE) {
           sb.append(format("  %s %20.8f %12d %12.3f\n", "Atomic Charges    ", permanentMultipoleEnergy,
               nPermanentInteractions, electrostaticTime * toSeconds));
         } else
           sb.append(format("  %s %20.8f %12d %12.3f\n", "Atomic Multipoles ", permanentMultipoleEnergy,
               nPermanentInteractions, electrostaticTime * toSeconds));
       }
     }
     if (polarizationTerm && nPermanentInteractions > 0) {
       sb.append(format("  %s %20.8f %12d %12.3f\n", "Polarization      ", polarizationEnergy,
           nPermanentInteractions, electrostaticTime * toSeconds));
     }
     if (generalizedKirkwoodTerm && nGKInteractions > 0) {
       sb.append(
           format("  %s %20.8f %12d\n", "Solvation         ", solvationEnergy, nGKInteractions));
     }
     if (relativeSolvationTerm) {
       sb.append(format("  %s %20.8f %12d\n", "Relative Solvation", relativeSolvationEnergy,
           nRelativeSolvations));
     }
     if (esvTerm) {
       sb.append(
           format("  %s %20.8f  %s\n", "ExtendedSystemBias", esvBias, esvSystem.getLambdaList()));
       sb.append(esvSystem.getBiasDecomposition());
     }
     if (nnTerm) {
       sb.append(format("  %s %20.8f %12d %12.3f\n", "Neural Network    ", nnEnergy, nAtoms,
           nnTime * toSeconds));
     }
     sb.append(
         format("  %s %20.8f  %s %12.3f (sec)", "Total Potential   ", totalEnergy, "(Kcal/mole)",
             totalTime * toSeconds));
     int nsymm = crystal.getUnitCell().spaceGroup.getNumberOfSymOps();
     if (nsymm > 1) {
       sb.append(format("\n  %s %20.8f", "Unit Cell         ", totalEnergy * nsymm));
     }
     if (crystal.getUnitCell() != crystal) {
       nsymm = crystal.spaceGroup.getNumberOfSymOps();
       sb.append(format("\n  %s %20.8f", "Replicates Cell   ", totalEnergy * nsymm));
     }
 
     return sb.toString();
   }
 
 
   /**
    * Log out all bonded energy terms.
    */
   public void logBondedTerms() {
     if (bondTerm && nBonds > 0) {
       logger.info("\n Bond Stretching Interactions:");
       Bond[] bonds = getBonds();
       for (Bond bond : bonds) {
         logger.info(" Bond \t" + bond.toString());
       }
     }
     if (angleTerm && nAngles > 0) {
       logger.info("\n Angle Bending Interactions:");
       Angle[] angles = getAngles();
       for (Angle angle : angles) {
         logger.info(" Angle \t" + angle.toString());
       }
     }
     if (stretchBendTerm && nStretchBends > 0) {
       logger.info("\n Stretch-Bend Interactions:");
       StretchBend[] stretchBends = getStretchBends();
       for (StretchBend stretchBend : stretchBends) {
         logger.info(" Stretch-Bend \t" + stretchBend.toString());
       }
     }
     if (ureyBradleyTerm && nUreyBradleys > 0) {
       logger.info("\n Urey-Bradley Interactions:");
       UreyBradley[] ureyBradleys = getUreyBradleys();
       for (UreyBradley ureyBradley : ureyBradleys) {
         logger.info("Urey-Bradley \t" + ureyBradley.toString());
       }
     }
     if (outOfPlaneBendTerm && nOutOfPlaneBends > 0) {
       logger.info("\n Out-of-Plane Bend Interactions:");
       OutOfPlaneBend[] outOfPlaneBends = getOutOfPlaneBends();
       for (OutOfPlaneBend outOfPlaneBend : outOfPlaneBends) {
         logger.info(" Out-of-Plane Bend \t" + outOfPlaneBend.toString());
       }
     }
     if (torsionTerm && nTorsions > 0) {
       logger.info("\n Torsion Angle Interactions:");
       Torsion[] torsions = getTorsions();
       for (Torsion torsion : torsions) {
         logger.info(" Torsion \t" + torsion.toString());
       }
     }
     if (piOrbitalTorsionTerm && nPiOrbitalTorsions > 0) {
       logger.info("\n Pi-Orbital Torsion Interactions:");
       PiOrbitalTorsion[] piOrbitalTorsions = getPiOrbitalTorsions();
       for (PiOrbitalTorsion piOrbitalTorsion : piOrbitalTorsions) {
         logger.info(" Pi-Torsion \t" + piOrbitalTorsion.toString());
       }
     }
     if (stretchTorsionTerm && nStretchTorsions > 0) {
       logger.info("\n Stretch-Torsion Interactions:");
       StretchTorsion[] stretchTorsions = getStretchTorsions();
       for (StretchTorsion stretchTorsion : stretchTorsions) {
         logger.info(" Stretch-Torsion \t" + stretchTorsion.toString());
       }
     }
     if (angleTorsionTerm && nAngleTorsions > 0) {
       logger.info("\n Angle-Torsion Interactions:");
       AngleTorsion[] angleTorsions = getAngleTorsions();
       for (AngleTorsion angleTorsion : angleTorsions) {
         logger.info(" Angle-Torsion \t" + angleTorsion.toString());
       }
     }
     if (torsionTorsionTerm && nTorsionTorsions > 0) {
       logger.info("\n Torsion-Torsion Interactions:");
       TorsionTorsion[] torsionTorsions = getTorsionTorsions();
       for (TorsionTorsion torsionTorsion : torsionTorsions) {
         logger.info(" Torsion-Torsion \t" + torsionTorsion.toString());
       }
     }
     if (improperTorsionTerm && nImproperTorsions > 0) {
       logger.info("\n Improper Interactions:");
       ImproperTorsion[] improperTorsions = getImproperTorsions();
       for (ImproperTorsion improperTorsion : improperTorsions) {
         logger.info(" Improper \t" + improperTorsion.toString());
       }
     }
     if (restrainDistanceTerm && nRestrainDistances > 0) {
       logger.info("\n Restrain Distance Interactions:");
       List<RestrainDistance> restrainDistances = getRestrainDistances(null);
       for (RestrainDistance restrainDistance : restrainDistances) {
         logger.info(" Restrain Distance \t" + restrainDistance.toString());
       }
     }
     if (restrainTorsionTerm && nRestrainTorsions > 0) {
       logger.info("\n Restrain Torsion Interactions:");
       for (Torsion restrainTorsion : restrainTorsions) {
         logger.info(" Restrain Torsion \t" + restrainTorsion.toString());
       }
     }
     if (restrainPositionTerm && nRestrainPositions > 0) {
       logger.info("\n Restrain Position Interactions:");
       for (RestrainPosition restrainPosition : restrainPositions) {
         logger.info(" Restrain Position \t" + restrainPosition.toString());
       }
     }
     if (restrainGroupTerm && nRestrainGroups > 0) {
       logger.info("\n Restrain Group Interactions:");
       logger.info(restrainGroups.toString());
     }
   }
 
   /**
    * Setter for the field <code>lambdaBondedTerms</code>.
    *
    * @param lambdaBondedTerms    a boolean.
    * @param lambdaAllBondedTerms a boolean.
    */
   void setLambdaBondedTerms(boolean lambdaBondedTerms, boolean lambdaAllBondedTerms) {
     this.lambdaBondedTerms = lambdaBondedTerms;
     this.lambdaAllBondedTerms = lambdaAllBondedTerms;
   }
 
   /**
    * Return the non-bonded components of energy (vdW, electrostatics).
    *
    * @param includeSolv Include solvation energy
    * @return Nonbonded energy
    */
   private double getNonbondedEnergy(boolean includeSolv) {
     return (includeSolv ? (totalNonBondedEnergy + solvationEnergy) : totalNonBondedEnergy);
   }
 
   /**
    * Private method for internal use, so we don't have subclasses calling super.energy, and this
    * class delegating to the subclass's getGradient method.
    *
    * @param g Gradient array to fill.
    * @return Gradient array.
    */
   private double[] fillGradient(double[] g) {
     assert (g != null);
     double[] grad = new double[3];
     int n = getNumberOfVariables();
     if (g == null || g.length < n) {
       g = new double[n];
     }
     int index = 0;
     for (int i = 0; i < nAtoms; i++) {
       Atom a = atoms[i];
       if (a.isActive()) {
         a.getXYZGradient(grad);
         double gx = grad[0];
         double gy = grad[1];
         double gz = grad[2];
         if (isNaN(gx) || isInfinite(gx) || isNaN(gy) || isInfinite(gy) || isNaN(gz) || isInfinite(
             gz)) {
           StringBuilder sb = new StringBuilder(
               format("The gradient of atom %s is (%8.3f,%8.3f,%8.3f).", a, gx, gy, gz));
           double[] vals = new double[3];
           a.getVelocity(vals);
           sb.append(format("\n Velocities: %8.3g %8.3g %8.3g", vals[0], vals[1], vals[2]));
           a.getAcceleration(vals);
           sb.append(format("\n Accelerations: %8.3g %8.3g %8.3g", vals[0], vals[1], vals[2]));
           a.getPreviousAcceleration(vals);
           sb.append(
               format("\n Previous accelerations: %8.3g %8.3g %8.3g", vals[0], vals[1], vals[2]));
 
           throw new EnergyException(sb.toString());
         }
         g[index++] = gx;
         g[index++] = gy;
         g[index++] = gz;
       }
     }
     return g;
   }
 
   /**
    * setRestrainDistance
    *
    * @param a1                a {@link ffx.potential.bonded.Atom} object.
    * @param a2                a {@link ffx.potential.bonded.Atom} object.
    * @param distance          a double.
    * @param forceConstant     the force constant in kcal/mole.
    * @param flatBottom        Radius of a flat-bottom potential in Angstroms.
    * @param lamStart          At what lambda does the restraint begin to take effect?
    * @param lamEnd            At what lambda does the restraint hit full strength?
    * @param switchingFunction Switching function to use as a lambda dependence.
    */
   private void setRestrainDistance(Atom a1, Atom a2, double distance, double forceConstant,
                                    double flatBottom, double lamStart, double lamEnd,
                                    UnivariateSwitchingFunction switchingFunction) {
     restrainDistanceTerm = true;
     boolean rbLambda = !(switchingFunction instanceof ConstantSwitch) && lambdaTerm;
     RestrainDistance restrainDistance = new RestrainDistance(a1, a2, crystal, rbLambda, lamStart, lamEnd, switchingFunction);
     int[] classes = {a1.getAtomType().atomClass, a2.getAtomType().atomClass};
     if (flatBottom != 0) {
       BondType bondType = new BondType(classes, forceConstant, distance,
           BondType.BondFunction.FLAT_BOTTOM_HARMONIC, flatBottom);
       restrainDistance.setBondType(bondType);
     } else {
       BondType bondType = new BondType(classes, forceConstant, distance,
           BondType.BondFunction.HARMONIC);
       restrainDistance.setBondType(bondType);
     }
 
     if (restrainDistances == null) {
       nRestrainDistances = 0;
     }
 
     RestrainDistance[] restrainDistances1 = new RestrainDistance[++nRestrainDistances];
     if (restrainDistances != null && restrainDistances.length != 0) {
       arraycopy(restrainDistances, 0, restrainDistances1, 0, (nRestrainDistances - 1));
     }
     restrainDistances1[nRestrainDistances - 1] = restrainDistance;
     restrainDistances = restrainDistances1;
     restrainDistance.energy(false);
     restrainDistance.log();
   }
 
   private Crystal configureNCS(ForceField forceField, Crystal unitCell) {
     // MTRIXn to be permuted with standard space group in NCSCrystal.java for experimental
     // refinement.
     if (forceField.getProperties().containsKey("MTRIX1")
         && forceField.getProperties().containsKey("MTRIX2") && forceField.getProperties()
         .containsKey("MTRIX3")) {
       Crystal unitCell2 = new Crystal(unitCell.a, unitCell.b, unitCell.c, unitCell.alpha,
           unitCell.beta, unitCell.gamma, unitCell.spaceGroup.pdbName);
       SpaceGroup spaceGroup = unitCell2.spaceGroup;
       // Separate string list MTRIXn into Double matricies then pass into symops
       CompositeConfiguration properties = forceField.getProperties();
       String[] MTRX1List = properties.getStringArray("MTRIX1");
       String[] MTRX2List = properties.getStringArray("MTRIX2");
       String[] MTRX3List = properties.getStringArray("MTRIX3");
       spaceGroup.symOps.clear();
       double number1;
       double number2;
       double number3;
       for (int i = 0; i < MTRX1List.length; i++) {
         double[][] Rot_MTRX = {{0, 0, 0}, {0, 0, 0}, {0, 0, 0}};
         double[] Tr_MTRX = {0, 0, 0};
         String[] tokens1 = MTRX1List[i].trim().split(" +"); // 4 items: rot [0][1-3] * trans[0]
         String[] tokens2 = MTRX2List[i].trim().split(" +"); // 4 items: rot [1][1-3] * trans[1]
         String[] tokens3 = MTRX3List[i].trim().split(" +"); // 4 items: rot [2][1-3] * trans[2]
         for (int k = 0; k < 4; k++) {
           number1 = Double.parseDouble(tokens1[k]);
           number2 = Double.parseDouble(tokens2[k]);
           number3 = Double.parseDouble(tokens3[k]);
           if (k != 3) {
             Rot_MTRX[0][k] = number1;
             Rot_MTRX[1][k] = number2;
             Rot_MTRX[2][k] = number3;
           } else {
             Tr_MTRX[0] = number1;
             Tr_MTRX[1] = number2;
             Tr_MTRX[2] = number3;
           }
         }
         SymOp symOp = new SymOp(Rot_MTRX, Tr_MTRX);
         if (logger.isLoggable(Level.FINEST)) {
           logger.info(
               format(" MTRIXn SymOp: %d of %d\n" + symOp, i + 1, MTRX1List.length));
         }
         spaceGroup.symOps.add(symOp);
       }
       unitCell = NCSCrystal.NCSCrystalFactory(unitCell, spaceGroup.symOps);
       unitCell.updateCrystal();
     }
     return unitCell;
   }
 
   /**
    * Getter for the field <code>restrainDistances</code>.
    *
    * @param bondFunction the type of bond function.
    * @return a {@link java.util.List} object.
    */
   public List<RestrainDistance> getRestrainDistances(@Nullable BondType.BondFunction bondFunction) {
     List<RestrainDistance> list = new ArrayList<>();
     if (restrainDistances != null && restrainDistances.length > 0) {
       // If the bondFunction is null, return all restrained bonds.
       if (bondFunction == null) {
         return Arrays.asList(restrainDistances);
       }
       // Otherwise, return only the restraint bonds with the specified bond function.
       for (RestrainDistance restrainDistance : restrainDistances) {
         if (restrainDistance.getBondType().bondFunction == bondFunction) {
           list.add(restrainDistance);
         }
       }
       if (!list.isEmpty()) {
         return list;
       }
     }
     return null;
   }
 
   public RestrainMode getRestrainMode() {
     return restrainMode;
   }
 
   /**
    * Getter for the field <code>restraintBonds</code>.
    *
    * @return a {@link java.util.List} object.
    */
   public Torsion[] getRestrainTorsions() {
     if (restrainTorsions != null && restrainTorsions.length > 0) {
       return restrainTorsions;
     } else {
       return null;
     }
   }
 
   /**
    * Getter for the RestrainGroup field.
    *
    * @return Returns RestrainGroup.
    */
   public RestrainGroups getRestrainGroups() {
     return restrainGroups;
   }
 
   private class BondedRegion extends ParallelRegion {
 
     // Shared RMSD variables.
     private final SharedDouble sharedBondRMSD;
     private final SharedDouble sharedAngleRMSD;
     // Shared force field bonded energy accumulation variables.
     private final SharedDouble sharedBondEnergy;
     private final SharedDouble sharedAngleEnergy;
     private final SharedDouble sharedOutOfPlaneBendEnergy;
     private final SharedDouble sharedPiOrbitalTorsionEnergy;
     private final SharedDouble sharedStretchBendEnergy;
     private final SharedDouble sharedUreyBradleyEnergy;
     private final SharedDouble sharedImproperTorsionEnergy;
     private final SharedDouble sharedTorsionEnergy;
     private final SharedDouble sharedStretchTorsionEnergy;
     private final SharedDouble sharedAngleTorsionEnergy;
     private final SharedDouble sharedTorsionTorsionEnergy;
     private final SharedDouble sharedRestrainPositionEnergy;
     private final SharedDouble sharedRestrainDistanceEnergy;
     private final SharedDouble sharedRestrainTorsionEnergy;
     // Number of threads.
     private final int nThreads;
     // Gradient loops.
     private final GradInitLoop[] gradInitLoops;
     private final GradReduceLoop[] gradReduceLoops;
     // Force field bonded energy parallel loops.
     private final BondedTermLoop[] bondLoops;
     private final BondedTermLoop[] angleLoops;
     private final BondedTermLoop[] outOfPlaneBendLoops;
     private final BondedTermLoop[] improperTorsionLoops;
     private final BondedTermLoop[] piOrbitalTorsionLoops;
     private final BondedTermLoop[] stretchBendLoops;
     private final BondedTermLoop[] torsionLoops;
     private final BondedTermLoop[] stretchTorsionLoops;
     private final BondedTermLoop[] angleTorsionLoops;
     private final BondedTermLoop[] torsionTorsionLoops;
     private final BondedTermLoop[] ureyBradleyLoops;
     private final BondedTermLoop[] restrainPositionLoops;
     private final BondedTermLoop[] restrainDistanceLoops;
     private final BondedTermLoop[] restrainTorsionLoops;
     private final AtomicDoubleArray3D grad;
     // Flag to indicate gradient computation.
     private boolean gradient = false;
     private AtomicDoubleArrayImpl atomicDoubleArrayImpl;
     private AtomicDoubleArray3D lambdaGrad;
 
     BondedRegion() {
 
       // Allocate shared RMSD variables.
       sharedAngleRMSD = new SharedDouble();
       sharedBondRMSD = new SharedDouble();
 
       // Allocate shared force field bonded energy variables.
       sharedBondEnergy = new SharedDouble();
       sharedAngleEnergy = new SharedDouble();
       sharedImproperTorsionEnergy = new SharedDouble();
       sharedOutOfPlaneBendEnergy = new SharedDouble();
       sharedPiOrbitalTorsionEnergy = new SharedDouble();
       sharedStretchBendEnergy = new SharedDouble();
       sharedTorsionEnergy = new SharedDouble();
       sharedStretchTorsionEnergy = new SharedDouble();
       sharedAngleTorsionEnergy = new SharedDouble();
       sharedTorsionTorsionEnergy = new SharedDouble();
       sharedUreyBradleyEnergy = new SharedDouble();
 
       // Allocate Restrain energy variables.
       sharedRestrainPositionEnergy = new SharedDouble();
       sharedRestrainDistanceEnergy = new SharedDouble();
       sharedRestrainTorsionEnergy = new SharedDouble();
 
       nThreads = parallelTeam.getThreadCount();
 
       // Gradient initialization loops.
       gradInitLoops = new GradInitLoop[nThreads];
       gradReduceLoops = new GradReduceLoop[nThreads];
 
       // Allocate memory for force field bonded energy loop arrays.
       angleLoops = new BondedTermLoop[nThreads];
       bondLoops = new BondedTermLoop[nThreads];
       improperTorsionLoops = new BondedTermLoop[nThreads];
       outOfPlaneBendLoops = new BondedTermLoop[nThreads];
       piOrbitalTorsionLoops = new BondedTermLoop[nThreads];
       stretchBendLoops = new BondedTermLoop[nThreads];
       torsionLoops = new BondedTermLoop[nThreads];
       stretchTorsionLoops = new BondedTermLoop[nThreads];
       angleTorsionLoops = new BondedTermLoop[nThreads];
       torsionTorsionLoops = new BondedTermLoop[nThreads];
       ureyBradleyLoops = new BondedTermLoop[nThreads];
       restrainPositionLoops = new BondedTermLoop[nThreads];
       restrainTorsionLoops = new BondedTermLoop[nThreads];
       restrainDistanceLoops = new BondedTermLoop[nThreads];
 
       // Define how the gradient will be accumulated.
       atomicDoubleArrayImpl = AtomicDoubleArrayImpl.MULTI;
       ForceField forceField = molecularAssembly.getForceField();
 
       String value = forceField.getString("ARRAY_REDUCTION", "MULTI");
       try {
         atomicDoubleArrayImpl = AtomicDoubleArrayImpl.valueOf(toEnumForm(value));
       } catch (Exception e) {
         logger.info(format(" Unrecognized ARRAY-REDUCTION %s; defaulting to %s", value,
             atomicDoubleArrayImpl));
       }
       logger.fine(format("  Bonded using %s arrays.", atomicDoubleArrayImpl.toString()));
 
       grad = new AtomicDoubleArray3D(atomicDoubleArrayImpl, nAtoms, nThreads);
       if (lambdaTerm) {
         lambdaGrad = new AtomicDoubleArray3D(atomicDoubleArrayImpl, nAtoms, nThreads);
       }
     }
 
     @Override
     public void finish() {
       // Finalize bond and angle RMSD values.
       if (bondTerm) {
         bondRMSD = sqrt(sharedBondRMSD.get() / bonds.length);
       }
       if (angleTerm) {
         angleRMSD = sqrt(sharedAngleRMSD.get() / angles.length);
       }
 
       // Load shared energy values into their respective fields.
       angleEnergy = sharedAngleEnergy.get();
       bondEnergy = sharedBondEnergy.get();
       improperTorsionEnergy = sharedImproperTorsionEnergy.get();
       outOfPlaneBendEnergy = sharedOutOfPlaneBendEnergy.get();
       piOrbitalTorsionEnergy = sharedPiOrbitalTorsionEnergy.get();
       stretchBendEnergy = sharedStretchBendEnergy.get();
       ureyBradleyEnergy = sharedUreyBradleyEnergy.get();
       torsionEnergy = sharedTorsionEnergy.get();
       stretchTorsionEnergy = sharedStretchTorsionEnergy.get();
       angleTorsionEnergy = sharedAngleTorsionEnergy.get();
       torsionTorsionEnergy = sharedTorsionTorsionEnergy.get();
       ureyBradleyEnergy = sharedUreyBradleyEnergy.get();
 
       // Load shared restrain energy values.
       restrainPositionEnergy = sharedRestrainPositionEnergy.get();
       restrainDistanceEnergy = sharedRestrainDistanceEnergy.get();
       restrainTorsionEnergy = sharedRestrainTorsionEnergy.get();
     }
 
     @Override
     public void run() throws Exception {
       int threadID = getThreadIndex();
 
       // Initialize the Gradient to zero.
       if (gradient) {
         if (gradInitLoops[threadID] == null) {
           gradInitLoops[threadID] = new GradInitLoop();
         }
         execute(0, nAtoms - 1, gradInitLoops[threadID]);
       }
 
       // Evaluate force field bonded energy terms in parallel.
       if (angleTerm) {
         if (angleLoops[threadID] == null) {
           angleLoops[threadID] = new BondedTermLoop(angles, sharedAngleEnergy, sharedAngleRMSD);
         }
         if (threadID == 0) {
           angleTime = -System.nanoTime();
         }
         execute(0, nAngles - 1, angleLoops[threadID]);
         if (threadID == 0) {
           angleTime += System.nanoTime();
         }
       }
 
       if (bondTerm) {
         if (bondLoops[threadID] == null) {
           bondLoops[threadID] = new BondedTermLoop(bonds, sharedBondEnergy, sharedBondRMSD);
         }
         if (threadID == 0) {
           bondTime = -System.nanoTime();
         }
         execute(0, nBonds - 1, bondLoops[threadID]);
         if (threadID == 0) {
           bondTime += System.nanoTime();
         }
       }
 
       if (improperTorsionTerm) {
         if (improperTorsionLoops[threadID] == null) {
           improperTorsionLoops[threadID] = new BondedTermLoop(improperTorsions,
               sharedImproperTorsionEnergy);
         }
         if (threadID == 0) {
           improperTorsionTime = -System.nanoTime();
         }
         execute(0, nImproperTorsions - 1, improperTorsionLoops[threadID]);
         if (threadID == 0) {
           improperTorsionTime += System.nanoTime();
         }
       }
 
       if (outOfPlaneBendTerm) {
         if (outOfPlaneBendLoops[threadID] == null) {
           outOfPlaneBendLoops[threadID] = new BondedTermLoop(outOfPlaneBends,
               sharedOutOfPlaneBendEnergy);
         }
         if (threadID == 0) {
           outOfPlaneBendTime = -System.nanoTime();
         }
         execute(0, nOutOfPlaneBends - 1, outOfPlaneBendLoops[threadID]);
         if (threadID == 0) {
           outOfPlaneBendTime += System.nanoTime();
         }
       }
 
       if (piOrbitalTorsionTerm) {
         if (piOrbitalTorsionLoops[threadID] == null) {
           piOrbitalTorsionLoops[threadID] = new BondedTermLoop(piOrbitalTorsions,
               sharedPiOrbitalTorsionEnergy);
         }
         if (threadID == 0) {
           piOrbitalTorsionTime = -System.nanoTime();
         }
         execute(0, nPiOrbitalTorsions - 1, piOrbitalTorsionLoops[threadID]);
         if (threadID == 0) {
           piOrbitalTorsionTime += System.nanoTime();
         }
       }
 
       if (stretchBendTerm) {
         if (stretchBendLoops[threadID] == null) {
           stretchBendLoops[threadID] = new BondedTermLoop(stretchBends, sharedStretchBendEnergy);
         }
         if (threadID == 0) {
           stretchBendTime = -System.nanoTime();
         }
         execute(0, nStretchBends - 1, stretchBendLoops[threadID]);
         if (threadID == 0) {
           stretchBendTime += System.nanoTime();
         }
       }
 
       if (torsionTerm) {
         if (torsionLoops[threadID] == null) {
           torsionLoops[threadID] = new BondedTermLoop(torsions, sharedTorsionEnergy);
         }
         if (threadID == 0) {
           torsionTime = -System.nanoTime();
         }
         execute(0, nTorsions - 1, torsionLoops[threadID]);
         if (threadID == 0) {
           torsionTime += System.nanoTime();
         }
       }
 
       if (stretchTorsionTerm) {
         if (stretchTorsionLoops[threadID] == null) {
           stretchTorsionLoops[threadID] = new BondedTermLoop(stretchTorsions,
               sharedStretchTorsionEnergy);
         }
         if (threadID == 0) {
           stretchTorsionTime = -System.nanoTime();
         }
         execute(0, nStretchTorsions - 1, stretchTorsionLoops[threadID]);
         if (threadID == 0) {
           stretchTorsionTime += System.nanoTime();
         }
       }
 
       if (angleTorsionTerm) {
         if (angleTorsionLoops[threadID] == null) {
           angleTorsionLoops[threadID] = new BondedTermLoop(angleTorsions, sharedAngleTorsionEnergy);
         }
         if (threadID == 0) {
           angleTorsionTime = -System.nanoTime();
         }
         execute(0, nAngleTorsions - 1, angleTorsionLoops[threadID]);
         if (threadID == 0) {
           angleTorsionTime += System.nanoTime();
         }
       }
 
       if (torsionTorsionTerm) {
         if (torsionTorsionLoops[threadID] == null) {
           torsionTorsionLoops[threadID] = new BondedTermLoop(torsionTorsions,
               sharedTorsionTorsionEnergy);
         }
         if (threadID == 0) {
           torsionTorsionTime = -System.nanoTime();
         }
         execute(0, nTorsionTorsions - 1, torsionTorsionLoops[threadID]);
         if (threadID == 0) {
           torsionTorsionTime += System.nanoTime();
         }
       }
 
       if (ureyBradleyTerm) {
         if (ureyBradleyLoops[threadID] == null) {
           ureyBradleyLoops[threadID] = new BondedTermLoop(ureyBradleys, sharedUreyBradleyEnergy);
         }
         if (threadID == 0) {
           ureyBradleyTime = -System.nanoTime();
         }
         execute(0, nUreyBradleys - 1, ureyBradleyLoops[threadID]);
         if (threadID == 0) {
           ureyBradleyTime += System.nanoTime();
         }
       }
 
       // Evaluate RestraintPosition terms in parallel.
       if ((restrainMode == RestrainMode.ENERGY) ||
           (restrainMode == RestrainMode.ALCHEMICAL && lambdaBondedTerms)) {
         boolean checkAlchemicalAtoms = (restrainMode == RestrainMode.ENERGY);
         if (restrainPositionTerm && nRestrainPositions > 0) {
           if (restrainPositionLoops[threadID] == null) {
             restrainPositionLoops[threadID] = new BondedTermLoop(restrainPositions, sharedRestrainPositionEnergy, null, checkAlchemicalAtoms);
           }
           if (threadID == 0) {
             restrainPositionTime = -System.nanoTime();
           }
           execute(0, nRestrainPositions - 1, restrainPositionLoops[threadID]);
           if (threadID == 0) {
             restrainPositionTime += System.nanoTime();
           }
         }
 
         // Evaluate RestrainDistance terms in parallel.
         if (restrainDistanceTerm && nRestrainDistances > 0) {
           if (restrainDistanceLoops[threadID] == null) {
             restrainDistanceLoops[threadID] = new BondedTermLoop(restrainDistances, sharedRestrainDistanceEnergy, null, checkAlchemicalAtoms);
           }
           if (threadID == 0) {
             restrainDistanceTime = -System.nanoTime();
           }
           execute(0, nRestrainDistances - 1, restrainDistanceLoops[threadID]);
           if (threadID == 0) {
             restrainDistanceTime += System.nanoTime();
           }
         }
 
         // Evaluate RestrainTorsion terms in parallel.
         if (restrainTorsionTerm && nRestrainTorsions > 0) {
           if (restrainTorsionLoops[threadID] == null) {
             restrainTorsionLoops[threadID] = new BondedTermLoop(restrainTorsions, sharedRestrainTorsionEnergy, null, checkAlchemicalAtoms);
           }
           if (threadID == 0) {
             restrainTorsionTime = -System.nanoTime();
           }
           execute(0, nRestrainTorsions - 1, restrainTorsionLoops[threadID]);
           if (threadID == 0) {
             restrainTorsionTime += System.nanoTime();
           }
         }
       }
 
       // Reduce the Gradient and load it into Atom instances.
       if (gradient) {
         if (gradReduceLoops[threadID] == null) {
           gradReduceLoops[threadID] = new GradReduceLoop();
         }
         execute(0, nAtoms - 1, gradReduceLoops[threadID]);
       }
     }
 
     public void setGradient(boolean gradient) {
       this.gradient = gradient;
     }
 
     @Override
     public void start() {
       // Zero out shared RMSD values.
       sharedAngleRMSD.set(0.0);
       sharedBondRMSD.set(0.0);
 
       // Zero out shared energy values.
       sharedAngleEnergy.set(0.0);
       sharedBondEnergy.set(0.0);
       sharedImproperTorsionEnergy.set(0.0);
       sharedOutOfPlaneBendEnergy.set(0.0);
       sharedPiOrbitalTorsionEnergy.set(0.0);
       sharedStretchBendEnergy.set(0.0);
       sharedTorsionEnergy.set(0.0);
       sharedStretchTorsionEnergy.set(0.0);
       sharedAngleTorsionEnergy.set(0.0);
       sharedTorsionTorsionEnergy.set(0.0);
       sharedUreyBradleyEnergy.set(0.0);
 
       // Zero out shared restraint energy values.
       sharedRestrainPositionEnergy.set(0.0);
       sharedRestrainDistanceEnergy.set(0.0);
       sharedRestrainTorsionEnergy.set(0.0);
 
       // Assure capacity of the gradient arrays.
       if (gradient) {
         grad.alloc(nAtoms);
       }
       if (lambdaTerm) {
         lambdaGrad.alloc(nAtoms);
       }
     }
 
     private class GradInitLoop extends IntegerForLoop {
 
       @Override
       public void run(int first, int last) {
         int threadID = getThreadIndex();
         if (gradient) {
           grad.reset(threadID, first, last);
           for (int i = first; i <= last; i++) {
             atoms[i].setXYZGradient(0.0, 0.0, 0.0);
           }
         }
         if (lambdaTerm) {
           lambdaGrad.reset(threadID, first, last);
           for (int i = first; i <= last; i++) {
             atoms[i].setLambdaXYZGradient(0.0, 0.0, 0.0);
           }
         }
       }
 
       @Override
       public IntegerSchedule schedule() {
         return IntegerSchedule.fixed();
       }
     }
 
     private class GradReduceLoop extends IntegerForLoop {
 
       @Override
       public void run(int first, int last) {
         if (gradient) {
           grad.reduce(first, last);
           for (int i = first; i <= last; i++) {
             Atom a = atoms[i];
             a.setXYZGradient(grad.getX(i), grad.getY(i), grad.getZ(i));
           }
         }
         if (lambdaTerm) {
           lambdaGrad.reduce(first, last);
           for (int i = first; i <= last; i++) {
             Atom a = atoms[i];
             a.setLambdaXYZGradient(lambdaGrad.getX(i), lambdaGrad.getY(i), lambdaGrad.getZ(i));
           }
         }
       }
 
       @Override
       public IntegerSchedule schedule() {
         return IntegerSchedule.fixed();
       }
     }
 
     private class BondedTermLoop extends IntegerForLoop {
 
       private final BondedTerm[] terms;
       private final SharedDouble sharedEnergy;
       private final SharedDouble sharedRMSD;
       private final boolean checkAlchemicalAtoms;
       private final boolean computeRMSD;
       private double localEnergy;
       private double localRMSD;
       private int threadID;
 
       BondedTermLoop(BondedTerm[] terms, SharedDouble sharedEnergy) {
         this(terms, sharedEnergy, null);
       }
 
       BondedTermLoop(BondedTerm[] terms, SharedDouble sharedEnergy, SharedDouble sharedRMSD) {
         this(terms, sharedEnergy, sharedRMSD, true);
       }
 
       BondedTermLoop(BondedTerm[] terms, SharedDouble sharedEnergy, SharedDouble sharedRMSD, boolean checkAlchemicalAtoms) {
         this.terms = terms;
         this.sharedEnergy = sharedEnergy;
         this.sharedRMSD = sharedRMSD;
         computeRMSD = (sharedRMSD != null);
         this.checkAlchemicalAtoms = checkAlchemicalAtoms;
       }
 
       @Override
       public void finish() {
         sharedEnergy.addAndGet(localEnergy);
         if (computeRMSD) {
           sharedRMSD.addAndGet(localRMSD);
         }
       }
 
       @Override
       public void run(int first, int last) {
         for (int i = first; i <= last; i++) {
           BondedTerm term = terms[i];
           boolean used = true;
           /*
            * The logic here deals with how DualTopologyEnergy (DTE) works.
            * If this ForceFieldEnergy (FFE) is not part of a DTE, lambdaBondedTerms is always false, and the term is always evaluated.
            *
            * Most bonded terms should be at full-strength, regardless of lambda, "complemented" to 1.0*strength.
            * Outside FFE, DTE scales the initial, !lambdaBondedTerms evaluation by f(lambda).
            *
            * In the case of a bonded term lacking any softcore atoms, this will be externally complemented by the other FFE topology.
            * If there is internal lambda-scaling, that will separately apply at both ends.
            *
            * In the case of a bonded term with a softcore atom, it's a bit trickier.
            * If it's unscaled by lambda, it needs to be internally complemented; we re-evaluate it with lambdaBondedTerms true.
            * This second evaluation is scaled by DTE by a factor of f(1-lambda), and becomes "restraintEnergy".
            * If it is scaled internally by lambda, we assume that the energy term is not meant to be internally complemented.
            * In that case, we skip evaluation into restraintEnergy.
            */
           if (checkAlchemicalAtoms) {
             used = !lambdaBondedTerms || lambdaAllBondedTerms || (term.applyLambda() && !term.isLambdaScaled());
           }
           if (used) {
             localEnergy += term.energy(gradient, threadID, grad, lambdaGrad);
             if (computeRMSD) {
               double value = term.getValue();
               localRMSD += value * value;
             }
           }
         }
       }
 
       @Override
       public void start() {
         localEnergy = 0.0;
         localRMSD = 0.0;
         threadID = getThreadIndex();
       }
     }
   }
 }