// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2024.
   //
   // This file is part of Force Field X.
   //
   // Force Field X is free software; you can redistribute it and/or modify it
  // under the terms of the GNU General Public License version 3 as published by
  // the Free Software Foundation.
  //
  // Force Field X is distributed in the hope that it will be useful, but WITHOUT
  // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
  // details.
  //
  // You should have received a copy of the GNU General Public License along with
  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
  //
  // Linking this library statically or dynamically with other modules is making a
  // combined work based on this library. Thus, the terms and conditions of the
  // GNU General Public License cover the whole combination.
  //
  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
  // executable, regardless of the license terms of these independent modules, and
  // to copy and distribute the resulting executable under terms of your choice,
  // provided that you also meet, for each linked independent module, the terms
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  // 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
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  package ffx.potential.nonbonded.implicit;
  
  import static ffx.numerics.atomic.AtomicDoubleArray.atomicDoubleArrayFactory;
  import static ffx.numerics.math.DoubleMath.add;
  import static ffx.numerics.math.DoubleMath.length2;
  import static ffx.numerics.math.DoubleMath.scale;
  import static ffx.numerics.math.DoubleMath.sub;
  import static java.lang.Double.compare;
  import static java.lang.String.format;
  import static org.apache.commons.math3.util.FastMath.PI;
  import static org.apache.commons.math3.util.FastMath.cbrt;
  import static org.apache.commons.math3.util.FastMath.exp;
  import static org.apache.commons.math3.util.FastMath.pow;
  
  import edu.rit.pj.IntegerForLoop;
  import edu.rit.pj.ParallelRegion;
  import edu.rit.pj.ParallelTeam;
  import edu.rit.pj.reduction.SharedDouble;
  import ffx.numerics.atomic.AtomicDoubleArray;
  import ffx.numerics.atomic.AtomicDoubleArray.AtomicDoubleArrayImpl;
  import ffx.numerics.atomic.AtomicDoubleArray3D;
  import ffx.potential.bonded.Atom;
  import ffx.potential.parameters.ForceField;
  
  import java.util.ArrayList;
  import java.util.Collections;
  import java.util.List;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  /**
   * GaussVol implements a description molecular volume and surface area described by overlapping
   * Gaussian spheres.
   *
   * <p>Ported from C++ code by Emilio Gallicchio. GaussVol is part of the AGBNP/OpenMM implicit
   * solvent model.
   *
   * @author Michael J. Schnieders
   * @see <a href="https://doi.org/10.1002/jcc.24745" target="_blank">
   * Zhang, B., Kilburg, D., Eastman, P., Pande, V. S., and Gallicchio, E. (2017).
   * Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units.
   * Journal of Computational Chemistry, 38(10), 740-752.</a>
   * @since 1.0
   */
  public class GaussVol {
  
    /* -------------------------------------------------------------------------- *
     *                                 GaussVol                                   *
     * -------------------------------------------------------------------------- *
     * This file is part of the AGBNP/OpenMM implicit solvent model software      *
     * implementation funded by the National Science Foundation under grant:      *
     * NSF SI2 1440665  "SI2-SSE: High-Performance Software for Large-Scale       *
     * Modeling of Binding Equilibria"                                            *
     *                                                                            *
     * copyright (c) 2016 Emilio Gallicchio                                       *
     * Authors: Emilio Gallicchio <egallicchio@brooklyn.cuny.edu>                 *
     * Contributors:                                                              *
     *                                                                            *
     *  AGBNP/OpenMM is free software: you can redistribute it and/or modify      *
     *  it under the terms of the GNU Lesser General Public License version 3     *
     *  as published by the Free Software Foundation.                             *
     *                                                                            *
    *  AGBNP/OpenMM 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 AGBNP/OpenMM.  If not, see <http://www.gnu.org/licenses/>      *
    *                                                                            *
    * -------------------------------------------------------------------------- */
 
   private static final Logger logger = Logger.getLogger(GaussVol.class.getName());
   /**
    * Finite-Difference step size to compute surface area.
    */
   private static final double offset = 0.005;
   /**
    * Conversion factor from a sphere to a Gaussian.
    */
   private static final double KFC = 2.2269859253;
 
   private static final double PFC = 2.5;
   /**
    * Set this to either KFC or PFC.
    */
   private static final double sphereConversion = KFC;
   /**
    * Maximum overlap level.
    */
   private static final int MAX_ORDER = 16;
   /**
    * Volume cutoffs for the switching function (A^3).
    */
   private static final double ANG3 = 1.0;
   /**
    * Volumes smaller than VOLMINA are switched to zero.
    */
   private static final double VOLMINA = 0.01 * ANG3;
   /**
    * Volumes larger than VOLMINB are not switched.
    */
   private static final double VOLMINB = 0.1 * ANG3;
   /**
    * Smallest positive double value.
    */
   private static final double MIN_GVOL = Double.MIN_VALUE;
 
   /**
    * Default offset applied to radii for use with Gaussian Volumes to correct for not including
    * hydrogen atoms.
    */
   public static final double DEFAULT_GAUSSVOL_RADII_OFFSET = 0.0;
   /**
    * Default scaling applied to radii for use with Gaussian Volumes to correct for not including
    * hydrogen atoms and general underestimation of molecular volume
    * <p>
    * Default set to 1.15 to match Corrigan et al. 2023 protein model
    * Can be set to greater than 1.0 to increase the radii by a uniform percentage
    * (ex: a radii scale of 1.25 increases all radii by 25%)
    */
   public static final double DEFAULT_GAUSSVOL_RADII_SCALE = 1.15;
 
   private static final double RMIN_TO_SIGMA = 1.0 / pow(2.0, 1.0 / 6.0);
 
   // Output Variables
   private final GaussVolRegion gaussVolRegion;
 
   private enum GAUSSVOL_MODE {COMPUTE_TREE, RESCAN_TREE}
 
   private final AtomicDoubleArray3D grad;
   private final SharedDouble totalVolume;
   private final SharedDouble energy;
   private final AtomicDoubleArray gradV;
   private final AtomicDoubleArray freeVolume;
   private final AtomicDoubleArray selfVolume;
   private final ParallelTeam parallelTeam;
 
   private final double vdwRadiiOffset;
   private final double vdwRadiiScale;
   private final boolean includeHydrogen;
   private final boolean useSigma;
   private static final double FOUR_THIRDS_PI = 4.0 / 3.0 * PI;
 
   /**
    * Array of Atoms in the system.
    */
   private final Atom[] atoms;
   /**
    * Number of atoms.
    */
   private final int nAtoms;
   /**
    * Atomic radii for all atoms.
    */
   private double[] radii;
   /**
    * Atomic volumes for all atoms, which are computed from atomic radii.
    */
   private double[] volumes;
   /**
    * All atomic radii with a small offset added, which are used to compute surface area using a
    * finite-difference approach.
    */
   private final double[] radiiOffset;
   /**
    * Atomic "self" volumes for all atoms, which are computed from the radii plus offset array.
    */
   private final double[] volumeOffset;
   /**
    * Surface tension -- in our implementation these values are kept at 1.0.
    */
   private final double[] gammas;
   /**
    * Flag to denote if an atom is a hydrogen, which results in it not contributing to the volume or
    * S.A.
    */
   private final boolean[] ishydrogen;
   /**
    * The self-volume fraction is the self-volume divided by the volume that ignores overlaps.
    */
   private final double[] selfVolumeFraction;
   /**
    * The Gaussian Overlap Tree.
    */
   private final GaussianOverlapTree tree;
   /**
    * Maximum depth that the tree reaches
    */
   private int maximumDepth = 0;
   /**
    * Total number of overlaps in overlap tree
    */
   private int totalNumberOfOverlaps = 0;
   /**
    * Surface area (Ang^2).
    */
   private double surfaceArea;
   /**
    * Volume (Ang^3).
    */
   private double volume;
   /**
    * The volume gradient, which does not include the solvent pressure constant (Ang^2).
    */
   private double[] volumeGradient;
   /**
    * The surface area gradient, which does not include the surface tension constant (Ang).
    */
   private double[] surfaceAreaGradient;
 
   /**
    * Creates/Initializes a GaussVol instance.
    *
    * @param atoms        The atoms to examine.
    * @param forceField   The ForceField in use.
    * @param parallelTeam ParallelTeam for Parallal jobs.
    */
   public GaussVol(Atom[] atoms, ForceField forceField, ParallelTeam parallelTeam) {
     this.atoms = atoms;
     nAtoms = atoms.length;
     tree = new GaussianOverlapTree(nAtoms);
     radii = new double[nAtoms];
     volumes = new double[nAtoms];
     gammas = new double[nAtoms];
     ishydrogen = new boolean[nAtoms];
     radiiOffset = new double[nAtoms];
     volumeOffset = new double[nAtoms];
     selfVolumeFraction = new double[nAtoms];
 
     vdwRadiiOffset = forceField.getDouble("GAUSSVOL_RADII_OFFSET", DEFAULT_GAUSSVOL_RADII_OFFSET);
     vdwRadiiScale = forceField.getDouble("GAUSSVOL_RADII_SCALE", DEFAULT_GAUSSVOL_RADII_SCALE);
     includeHydrogen = forceField.getBoolean("GAUSSVOL_HYDROGEN", false);
     useSigma = forceField.getBoolean("GAUSSVOL_USE_SIGMA", false);
 
     for (int i = 0; i < nAtoms; i++) {
       updateAtom(i);
     }
 
     this.parallelTeam = parallelTeam;
     int nThreads = 1;
     if (parallelTeam != null) {
       nThreads = parallelTeam.getThreadCount();
       gaussVolRegion = new GaussVolRegion(nThreads);
     } else {
       gaussVolRegion = null;
     }
 
     totalVolume = new SharedDouble();
     energy = new SharedDouble();
     AtomicDoubleArrayImpl atomicDoubleArrayImpl = AtomicDoubleArrayImpl.MULTI;
     grad = new AtomicDoubleArray3D(atomicDoubleArrayImpl, nAtoms, nThreads);
     gradV = atomicDoubleArrayFactory(atomicDoubleArrayImpl, nThreads, nAtoms);
     freeVolume = atomicDoubleArrayFactory(atomicDoubleArrayImpl, nThreads, nAtoms);
     selfVolume = atomicDoubleArrayFactory(atomicDoubleArrayImpl, nThreads, nAtoms);
   }
 
   /**
    * Get the radii.
    *
    * @return Returns the radii.
    */
   public double[] getRadii() {
     return radii;
   }
 
   /**
    * Overlap between two Gaussians represented by a (V,c,a) triplet
    *
    * <p>V: volume of Gaussian c: position of Gaussian a: exponential coefficient
    *
    * <p>g(x) = V (a/pi)^(3/2) exp(-a(x-c)^2)
    *
    * <p>this version is based on V=V(V1,V2,r1,r2,alpha) alpha = (a1 + a2)/(a1 a2)
    *
    * <p>dVdr is (1/r)*(dV12/dr) dVdV is dV12/dV1 dVdalpha is dV12/dalpha d2Vdalphadr is
    * (1/r)*d^2V12/dalpha dr d2VdVdr is (1/r) d^2V12/dV1 dr
    *
    * @param g1   Gaussian 1.
    * @param g2   Gaussian 2.
    * @param g12  Overlap Gaussian.
    * @param dVdr is (1/r)*(dV12/dr)
    * @param dVdV is dV12/dV1
    * @param sfp  Derivative of volume.
    * @return Volume.
    */
   private static double overlapGaussianAlpha(
       GaussianVca g1, GaussianVca g2, GaussianVca g12, double[] dVdr, double[] dVdV, double[] sfp) {
     double[] c1 = g1.c;
     double[] c2 = g2.c;
     double[] dist = new double[3];
 
     sub(c2, c1, dist);
     double d2 = length2(dist);
     double a12 = g1.a + g2.a;
     double deltai = 1.0 / a12;
 
     // 1/alpha
     double df = (g1.a) * (g2.a) * deltai;
     double ef = exp(-df * d2);
     double gvol = ((g1.v * g2.v) / pow(PI / df, 1.5)) * ef;
 
     // (1/r)*(dV/dr) w/o switching function
     double dgvol = -2.0 * df * gvol;
     dVdr[0] = dgvol;
 
     // (1/r)*(dV/dr) w/o switching function
     double dgvolv = g1.v > 0.0 ? gvol / g1.v : 0.0;
     dVdV[0] = dgvolv;
 
     // Parameters for overlap gaussian.
     // Note that c1 and c2 are Vec3's, and the "*" operator wants the vector first and scalar
     // second:
     // vector2 = vector1 * scalar
     // g12.c = ((c1 * g1.a) + (c2 * g2.a)) * deltai;
     double[] c1a = new double[3];
     double[] c2a = new double[3];
     scale(c1, g1.a * deltai, c1a);
     scale(c2, g2.a * deltai, c2a);
     add(c1a, c2a, g12.c);
     g12.a = a12;
     g12.v = gvol;
 
     // Switching function
     double[] sp = new double[1];
     double s = switchingFunction(gvol, VOLMINA, VOLMINB, sp);
     sfp[0] = sp[0] * gvol + s;
     return s * gvol;
   }
 
   /**
    * Overlap volume switching function and 1st derivative.
    *
    * @param gvol    Gaussian volume.
    * @param volmina Volume is zero below this limit.
    * @param volminb Volume is not switched above this limit.
    * @param sp      Switch first derivative.
    * @return Switch value.
    */
   private static double switchingFunction(
       double gvol, double volmina, double volminb, double[] sp) {
     if (gvol > volminb) {
       sp[0] = 0.0;
       return 1.0;
     } else if (gvol < volmina) {
       sp[0] = 0.0;
       return 0.0;
     }
     double swd = 1.0 / (volminb - volmina);
     double swu = (gvol - volmina) * swd;
     double swu2 = swu * swu;
     double swu3 = swu * swu2;
     sp[0] = swd * 30.0 * swu2 * (1.0 - 2.0 * swu + swu2);
     return swu3 * (10.0 - 15.0 * swu + 6.0 * swu2);
   }
 
   /**
    * Return the self volume fraction for each atom.
    *
    * @return The self-volume fractions.
    */
   public double[] getSelfVolumeFractions() {
     return selfVolumeFraction;
   }
 
   /**
    * Compute molecular volume and surface area.
    *
    * @param positions Atomic positions to use.
    * @return The volume.
    */
   public double computeVolumeAndSA(double[][] positions) {
 
     if (parallelTeam == null || parallelTeam.getThreadCount() == 1) {
       // Execute in the current thread.
       for (int i = 0; i < nAtoms - 1; i++) {
         updateAtom(i);
       }
 
       // Update the overlap tree.
       computeTree(positions);
 
       // Compute the volume.
       computeVolume(totalVolume, energy, grad, gradV, freeVolume, selfVolume);
     } else {
       // Execute in parallel.
       try {
         gaussVolRegion.init(GAUSSVOL_MODE.COMPUTE_TREE, positions);
         parallelTeam.execute(gaussVolRegion);
       } catch (Exception e) {
         logger.severe(" Exception evaluating GaussVol " + e);
       }
     }
 
     if (volumeGradient == null || volumeGradient.length != nAtoms * 3) {
       volumeGradient = new double[nAtoms * 3];
       surfaceAreaGradient = new double[nAtoms * 3];
     }
 
     double selfVolumeSum = 0.0;
     double noOverlapVolume = 0.0;
     for (int i = 0; i < nAtoms; i++) {
       double si = selfVolume.get(i);
       selfVolumeSum += si;
       double x = grad.getX(i);
       double y = grad.getY(i);
       double z = grad.getZ(i);
       if (ishydrogen[i]) {
         x = 0.0;
         y = 0.0;
         z = 0.0;
         selfVolumeFraction[i] = 0.0;
       } else {
         double vi = volumes[i];
         noOverlapVolume += vi;
         selfVolumeFraction[i] = si / vi;
       }
       // Volume based gradient
       int index = i * 3;
       volumeGradient[index++] = x;
       volumeGradient[index++] = y;
       volumeGradient[index] = z;
 
       // Surface Area based gradient
       index = i * 3;
       surfaceAreaGradient[index++] = x;
       surfaceAreaGradient[index++] = y;
       surfaceAreaGradient[index] = z;
     }
 
     // Log out the perfect self-volumes.
     if (logger.isLoggable(Level.FINE)) {
       double meanHCT = selfVolumeSum / noOverlapVolume;
       logger.fine(format("\n Mean Self-Volume Fraction: %16.8f", meanHCT));
       logger.fine(format(" Cube Root of the Fraction: %16.8f", cbrt(meanHCT)));
       if (logger.isLoggable(Level.FINEST)) {
         logger.finest(" Atomic Self-volume Fractions");
         for (int i = 0; i < nAtoms; i++) {
           logger.finest(format(" %6d %16.8f", i + 1, selfVolumeFraction[i]));
         }
       }
     }
 
     // Save the total molecular volume.
     volume = totalVolume.get();
 
     // Save a reference to non-offset radii and volumes.
     double[] radiiBak = this.radii;
     double[] volumeBak = this.volumes;
 
     // Load the offset radii and volumes.
     this.radii = radiiOffset;
     this.volumes = volumeOffset;
 
     // Run the volume calculation on radii that are slightly offset
     // for finite difference calculation of surface area.
 
     if (parallelTeam == null || parallelTeam.getThreadCount() == 1) {
       // Execute in the current thread.
       // Rescan the overlap tree.
       rescanTreeVolumes(positions);
       // Compute the volume.
       computeVolume(totalVolume, energy, grad, gradV, freeVolume, selfVolume);
     } else {
       // Execute in parallel.
       try {
         gaussVolRegion.init(GAUSSVOL_MODE.RESCAN_TREE, positions);
         parallelTeam.execute(gaussVolRegion);
       } catch (Exception e) {
         logger.severe(" Exception evaluating GaussVol " + e);
       }
     }
 
     // Set the radii and volumes to their non-offset values.
     this.radii = radiiBak;
     this.volumes = volumeBak;
 
     double selfVolumeOffsetSum = 0;
     for (int i = 0; i < nAtoms; i++) {
       selfVolumeOffsetSum += selfVolume.get(i);
       double x = grad.getX(i);
       double y = grad.getY(i);
       double z = grad.getZ(i);
       if (ishydrogen[i]) {
         x = 0.0;
         y = 0.0;
         z = 0.0;
       }
       // Surface Area based gradient
       int index = i * 3;
       surfaceAreaGradient[index] = (x - surfaceAreaGradient[index++]) / offset;
       surfaceAreaGradient[index] = (y - surfaceAreaGradient[index++]) / offset;
       surfaceAreaGradient[index] = (z - surfaceAreaGradient[index]) / offset;
     }
 
     // Calculate the surface area.
     surfaceArea = (selfVolumeOffsetSum - selfVolumeSum) / offset;
 
     return volume;
   }
 
   /**
    * Returns the maximum depth of the overlap tree
    *
    * @return maximumDepth
    */
   public int getMaximumDepth() {
     return maximumDepth;
   }
 
   /**
    * Return Surface Area (A^2).
    *
    * @return Surface Area (A^2).
    */
   public double getSurfaceArea() {
     return surfaceArea;
   }
 
   public double[] getSurfaceAreaGradient() {
     return surfaceAreaGradient;
   }
 
   /**
    * Return the total number of overlaps in the tree
    *
    * @return totalNumberOfOverlaps
    */
   public int getTotalNumberOfOverlaps() {
     return totalNumberOfOverlaps;
   }
 
   /**
    * Return Volume (A^3).
    *
    * @return Volume (A^3).
    */
   public double getVolume() {
     return volume;
   }
 
   public double[] getVolumeGradient() {
     return volumeGradient;
   }
 
   public void allocate(Atom[] atoms) throws Exception {
     if (atoms.length != this.atoms.length) {
       throw new Exception(" allocate: number of atoms does not match");
     }
   }
 
   /**
    * Constructs the tree.
    *
    * @param positions Current atomic positions.
    */
   private void computeTree(double[][] positions) {
     tree.computeOverlapTreeR(positions, radii, volumes, gammas, ishydrogen);
   }
 
   /**
    * Returns GaussVol volume energy function and forces. Also returns gradients with respect to
    * atomic volumes and atomic free-volumes and self-volumes.
    *
    * @param totalVolume Total volume.
    * @param totalEnergy Total energy.
    * @param grad        Atomic gradient.
    * @param gradV       Volume gradient.
    * @param freeVolume  Free volume.
    * @param selfVolume  Self volume.
    */
   private void computeVolume(
       SharedDouble totalVolume,
       SharedDouble totalEnergy,
       AtomicDoubleArray3D grad,
       AtomicDoubleArray gradV,
       AtomicDoubleArray freeVolume,
       AtomicDoubleArray selfVolume) {
     // Initialize output variables.
     totalVolume.set(0.0);
     totalEnergy.set(0.0);
     grad.reset(0, 0, nAtoms - 1);
     gradV.reset(0, 0, nAtoms - 1);
     freeVolume.reset(0, 0, nAtoms - 1);
     selfVolume.reset(0, 0, nAtoms - 1);
 
     // Compute the volume.
     tree.computeVolume2R(totalVolume, totalEnergy, grad, gradV, freeVolume, selfVolume);
 
     // Reduce output variables.
     grad.reduce(0, nAtoms - 1);
     gradV.reduce(0, nAtoms - 1);
     freeVolume.reduce(0, nAtoms - 1);
     selfVolume.reduce(0, nAtoms - 1);
 
     for (int i = 0; i < nAtoms; ++i) {
       if (volumes[i] > 0) {
         gradV.set(0, i, gradV.get(i) / volumes[i]);
       }
     }
   }
 
   /**
    * Rescan the tree after resetting gammas, radii and volumes.
    *
    * @param positions Atomic coordinates.
    */
   private void rescanTreeVolumes(double[][] positions) {
     tree.rescanTreeV(positions, radii, volumes, gammas, ishydrogen);
   }
 
   /**
    * Rescan the tree resetting gammas only with current values.
    */
   private void rescanTreeGammas() {
     tree.rescanTreeG(gammas);
   }
 
   /**
    * Returns number of overlaps for each atom.
    *
    * @param nov Number of overlaps.
    */
   private void getStats(int[] nov) {
     if (nov.length != nAtoms) {
       return;
     }
 
     for (int i = 0; i < nAtoms; i++) {
       nov[i] = 0;
     }
     for (int atom = 0; atom < nAtoms; atom++) {
       int slot = atom + 1;
       nov[atom] = tree.nChildrenUnderSlotR(slot);
     }
   }
 
   /**
    * Print the tree.
    */
   private void printTree() {
     tree.printTree();
   }
 
   /**
    * 3D Gaussian, V,c,a representation.
    */
   private static class GaussianVca {
 
     // Gaussian volume
     public double v;
     // Gaussian exponent
     public double a;
     // Center
     public double[] c = new double[3];
   }
 
   /**
    * Overlap between two Gaussians represented by a (V,c,a) triplet V: volume of Gaussian c: position
    * of Gaussian a: exponential coefficient
    *
    * <p>g(x) = V (a/pi)^(3/2) exp(-a(x-c)^2)
    *
    * <p>This version is based on V=V(V1,V2,r1,r2,alpha) alpha = (a1 + a2)/(a1 a2) dVdr is
    * (1/r)*(dV12/dr) dVdV is dV12/dV1 dVdalpha is dV12/dalpha d2Vdalphadr is (1/r)*d^2V12/dalpha dr
    * d2VdVdr is (1/r) d^2V12/dV1 dr
    */
   private static class GaussianOverlap implements Comparable<GaussianOverlap> {
 
     /**
      * level (0=root, 1=atoms, 2=2-body, 3=3-body, etc.)
      */
     public int level;
     /**
      * Gaussian representing overlap
      */
     public GaussianVca g;
     /**
      * Volume of overlap (also stores Psi1..i in GPU version)
      */
     public double volume;
     /**
      * The atomic index of the last atom of the overlap list (i, j, k, ..., atom)
      */
     public int atom;
     /**
      * Derivative wrt volume of first atom (also stores F1..i in GPU version)
      */
     double dvv1;
     /**
      * Derivative wrt position of first atom (also stores P1..i in GPU version)
      */
     double[] dv1;
     /**
      * Sum gammai for this overlap (surface tension parameter)
      */
     double gamma1i;
     /**
      * Self volume accumulator (also stores Psi'1..i in GPU version)
      */
     double selfVolume;
     /**
      * Switching function derivatives
      */
     double sfp;
     /**
      * = (Parent, atom) index in tree list of parent overlap
      */
     int parentIndex;
     /**
      * Start index in tree array of children
      */
     int childrenStartIndex;
     /**
      * Number of children.
      */
     int childrenCount;
 
     public GaussianOverlap() {
       g = new GaussianVca();
       dv1 = new double[3];
     }
 
     public GaussianOverlap(GaussianVca g, double volume, double selfVolume, int atom) {
       this.g = g;
       this.volume = volume;
       this.selfVolume = selfVolume;
       this.atom = atom;
 
       dv1 = new double[3];
     }
 
     /**
      * Order by volume, larger first.
      *
      * @param o GaussianOverlap to compare to.
      * @return Compare by volume.
      */
     @Override
     public int compareTo(GaussianOverlap o) {
       return compare(volume, o.volume);
     }
 
     /**
      * Print overlaps.
      */
     public void printOverlap() {
       logger.info(format(" Gaussian Overlap %d: Atom: %d, Parent: %d, ChildrenStartIndex: %d, ChildrenCount: %d,"
               + "Volume: %6.3f, Gamma: %6.3f, Gauss.a: %6.3f, Gauss.v: %6.3f, Gauss.center (%6.3f,%6.3f,%6.3f),"
               + "dedx: %6.3f, dedy: %6.3f, dedz: %6.3f, sfp: %6.3f",
           level, atom, parentIndex, childrenStartIndex, childrenCount, volume, gamma1i,
           g.a, g.v, g.c[0], g.c[1], g.c[2], dv1[0], dv1[1], dv1[2], sfp));
     }
   }
 
   public void updateAtom(int i) {
     Atom atom = atoms[i];
     ishydrogen[i] = atom.isHydrogen();
     if (includeHydrogen) {
       ishydrogen[i] = false;
     }
     radii[i] = atom.getVDWType().radius / 2.0;
     if (useSigma) {
       radii[i] *= RMIN_TO_SIGMA;
     }
     radii[i] += vdwRadiiOffset;
     radii[i] *= vdwRadiiScale;
     volumes[i] = FOUR_THIRDS_PI * pow(radii[i], 3);
     gammas[i] = 1.0;
     radiiOffset[i] = radii[i] + offset;
     volumeOffset[i] = FOUR_THIRDS_PI * pow(radiiOffset[i], 3);
   }
 
   /**
    * Gaussian Overlap Tree.
    */
   private class GaussianOverlapTree {
 
     /**
      * Number of atoms.
      */
     int nAtoms;
     /**
      * The root is at index 0. Atoms are from 1 .. nAtoms.
      */
     List<GaussianOverlap> overlaps;
 
     /**
      * GaussianOverlapTree constructor.
      *
      * @param nAtoms Number of atoms.
      */
     GaussianOverlapTree(int nAtoms) {
       this.nAtoms = nAtoms;
       overlaps = Collections.synchronizedList(new ArrayList<>(nAtoms + 1));
     }
 
     /**
      * Initialize the Overlap Tree.
      *
      * @param pos        Atomic positions.
      * @param radii      Atomic radii.
      * @param volumes    Atomic volumes.
      * @param gammas     Atomic surface tensions.
      * @param ishydrogen True if the atom is a hydrogen.
      */
     void initOverlapTree(
         double[][] pos, double[] radii, double[] volumes, double[] gammas, boolean[] ishydrogen) {
 
       // Reset tree
       overlaps = Collections.synchronizedList(new ArrayList<>(nAtoms + 1));
 
       // Slot 0 contains the master tree information, children = all of the atoms.
       GaussianOverlap overlap = new GaussianOverlap();
       overlap.level = 0;
       overlap.volume = 0;
       overlap.dvv1 = 0.;
       overlap.selfVolume = 0;
       overlap.sfp = 1.;
       overlap.gamma1i = 0.;
       overlap.parentIndex = -1;
       overlap.atom = -1;
       overlap.childrenStartIndex = 1;
       overlap.childrenCount = nAtoms;
       overlaps.add(0, overlap);
 
       // List of atoms start at slot 1.
       for (int iat = 0; iat < nAtoms; iat++) {
         overlap = new GaussianOverlap();
         double a = sphereConversion / (radii[iat] * radii[iat]);
         double vol = ishydrogen[iat] ? 0 : volumes[iat];
         overlap.level = 1;
         overlap.g.v = vol;
         overlap.g.a = a;
         overlap.g.c = pos[iat];
         overlap.volume = vol;
         overlap.dvv1 = 1; // dVi/dVi
         overlap.selfVolume = 0;
         overlap.sfp = 1;
         overlap.gamma1i = gammas[iat]; // gamma[iat] / SA_DR;
         overlap.parentIndex = 0;
         overlap.atom = iat;
         overlap.childrenStartIndex = -1;
         overlap.childrenCount = -1;
         overlaps.add(iat + 1, overlap);
       }
     }
 
     /**
      * Add Children.
      *
      * @param parentIndex      Parent index.
      * @param childrenOverlaps Children overlaps.
      * @return Index of the first added child.
      */
     int addChildren(int parentIndex, List<GaussianOverlap> childrenOverlaps) {
 
       // Adds children starting at the last slot
       int startIndex = overlaps.size();
 
       int noverlaps = childrenOverlaps.size();
 
       // Retrieves address of root overlap
       GaussianOverlap root = overlaps.get(parentIndex);
 
       // Registers list of children
       root.childrenStartIndex = startIndex;
       root.childrenCount = noverlaps;
 
       // Sort neighbors by overlap volume.
       Collections.sort(childrenOverlaps);
 
       int rootLevel = root.level;
       int nextLevel = rootLevel + 1;
 
       // Now copies the children overlaps from temp buffer.
       for (GaussianOverlap child : childrenOverlaps) {
         child.level = nextLevel;
 
         // Connect overlap to parent
         child.parentIndex = parentIndex;
 
         // Reset its children indexes
         child.childrenStartIndex = -1;
         child.childrenCount = -1;
 
         // Add to tree.
         overlaps.add(child);
       }
 
       return startIndex;
     }
 
     /**
      * Scans the siblings of overlap identified by "rootIndex" to create children overlaps, returns
      * them into the "childrenOverlaps" buffer: (root) + (atom) -> (root, atom)
      *
      * @param rootIndex        Root index.
      * @param childrenOverlaps Children overlaps.
      */
     void computeChildren(int rootIndex, List<GaussianOverlap> childrenOverlaps) {
       int parentIndex;
       int siblingStart, siblingCount;
 
       // Reset output buffer
       childrenOverlaps.clear();
 
       // Retrieves overlap.
       GaussianOverlap root = overlaps.get(rootIndex);
 
       // Retrieves parent overlap.
       parentIndex = root.parentIndex;
 
       // Master root? can't do computeChildren() on master root
       if (parentIndex < 0) {
         throw new IllegalArgumentException(" Cannot compute children of master node!");
       }
 
       if (root.level >= MAX_ORDER) {
         return; // Ignore overlaps above a certain order to cap computational cost.
       }
 
       GaussianOverlap parent = overlaps.get(parentIndex);
 
       // Retrieves start index and count of siblings. Includes both younger and older siblings
       siblingStart = parent.childrenStartIndex;
       siblingCount = parent.childrenCount;
 
       // Parent is not initialized?
       if (siblingStart < 0 || siblingCount < 0) {
         throw new IllegalArgumentException(
             format(" Parent %s of overlap %s has no sibilings.", parent, root));
       }
 
       // This overlap somehow is not the child of registered parent.
       if (rootIndex < siblingStart && rootIndex > siblingStart + siblingCount - 1) {
         throw new IllegalArgumentException(
             format(" Node %s is somehow not the child of its parent %s", root, parent));
       }
 
       // Now loops over "younger" siblings (i<j loop) to compute new overlaps.
       // Loop starts at the first younger sibling, and runs to the end of all siblings.
       for (int slotj = rootIndex + 1; slotj < siblingStart + siblingCount; slotj++) {
 
         GaussianVca g12 = new GaussianVca();
 
         GaussianOverlap sibling = overlaps.get(slotj);
         double gvol;
         double[] dVdr = new double[1];
         double[] dVdV = new double[1];
         double[] sfp = new double[1];
 
         // Atomic gaussian of last atom of sibling.
         int atom2 = sibling.atom;
         GaussianVca g1 = root.g;
 
         // Atoms are stored in the tree at indexes 1...N
         GaussianVca g2 = overlaps.get(atom2 + 1).g;
         gvol = overlapGaussianAlpha(g1, g2, g12, dVdr, dVdV, sfp);
 
         /*
          Create child if overlap volume is above a threshold.
          Due to infinite support, the Gaussian volume is never zero.
         */
         if (gvol > MIN_GVOL) {
           GaussianOverlap ov = new GaussianOverlap(g12, gvol, 0.0, atom2);
           // dv1 is the gradient of V(123..)n with respect to the position of 1
           // ov.dv1 = ( g2.c - g1.c ) * (-dVdr);
           sub(g2.c, g1.c, ov.dv1);
           scale(ov.dv1, -dVdr[0], ov.dv1);
 
           // dvv1 is the derivative of V(123...)n with respect to V(123...)
           ov.dvv1 = dVdV[0];
           ov.sfp = sfp[0];
           ov.gamma1i = root.gamma1i + overlaps.get(atom2 + 1).gamma1i;
           childrenOverlaps.add(ov);
         }
       }
     }
 
     /**
      * Grow the tree with more children starting at the given root slot (recursive).
      *
      * @param root The root index.
      */
     private void computeAndAddChildrenR(int root) {
       List<GaussianOverlap> childrenOverlaps = Collections.synchronizedList(new ArrayList<>());
       computeChildren(root, childrenOverlaps);
       int nOverlaps = childrenOverlaps.size();
       if (nOverlaps > 0) {
         int startSlot = addChildren(root, childrenOverlaps);
         for (int ichild = startSlot; ichild < startSlot + nOverlaps; ichild++) {
           computeAndAddChildrenR(ichild);
           totalNumberOfOverlaps++;
         }
       }
     }
 
     /**
      * Compute the overlap tree.
      *
      * @param pos        Atomic positions.
      * @param radii      Atomic radii.
      * @param volumes    Atomic volumes.
      * @param gammas     Atomic surface tensions.
      * @param ishydrogen True if the atom is a hydrogen.
      */
     void computeOverlapTreeR(
         double[][] pos, double[] radii, double[] volumes, double[] gammas, boolean[] ishydrogen) {
       initOverlapTree(pos, radii, volumes, gammas, ishydrogen);
       for (int slot = 1; slot <= nAtoms; slot++) {
         computeAndAddChildrenR(slot);
         totalNumberOfOverlaps++;
       }
     }
 
     /**
      * Compute volumes, energy of the overlap at slot and calls itself recursively to get the volumes
      * of the children.
      *
      * @param slot       Slot to begin from.
      * @param psi1i      Subtree accumulator for free volume.
      * @param f1i        Subtree accumulator for free volume.
      * @param p1i        Subtree accumulator for free volume.
      * @param psip1i     Subtree accumulator for self volume.
      * @param fp1i       Subtree accumulators for self volume.
      * @param pp1i       Subtree accumulators for self volume.
      * @param energy1i   Subtree accumulator for volume-based energy.
      * @param fenergy1i  Subtree accumulator for volume-based energy.
      * @param penergy1i  subtree accumulator for volume-based energy.
      * @param threadID   Thread for accumulation.
      * @param dr         Gradient of volume-based energy wrt to atomic positions.
      * @param dv         Gradient of volume-based energy wrt to atomic volumes.
      * @param freeVolume Atomic free volumes.
      * @param selfVolume Atomic self volumes.
      */
     void computeVolumeUnderSlot2R(
         int slot,
         double[] psi1i,
         double[] f1i,
         double[] p1i,
         double[] psip1i,
         double[] fp1i,
         double[] pp1i,
         double[] energy1i,
         double[] fenergy1i,
         double[] penergy1i,
         int threadID,
         AtomicDoubleArray3D dr,
         AtomicDoubleArray dv,
         AtomicDoubleArray freeVolume,
         AtomicDoubleArray selfVolume) {
 
       GaussianOverlap ov = overlaps.get(slot);
       // Keep track of overlap depth for each overlap.
       // If a new depth is greater than previous greatest, save depth in maximumDepth
       if (ov.level >= maximumDepth) {
         maximumDepth = ov.level;
       }
 
       // Whether to add volumes (e.g. selfs, 3-body overlaps) or subtract them (e.g. 2-body
       // overlaps, 4-body overlaps)
       double cf = ov.level % 2 == 0 ? -1.0 : 1.0;
       // Overall volume is increased/decreased by the full volume.
       double volcoeff = ov.level > 0 ? cf : 0;
       // Atomic contributions to overlap volume are evenly distributed.
       double volcoeffp = ov.level > 0 ? volcoeff / (double) ov.level : 0;
 
       int atom = ov.atom;
       double ai = overlaps.get(atom + 1).g.a;
       double a1i = ov.g.a;
       double a1 = a1i - ai;
 
       // For free volumes
       psi1i[0] = volcoeff * ov.volume;
       f1i[0] = volcoeff * ov.sfp;
 
       // For self volumes
       psip1i[0] = volcoeffp * ov.volume;
       fp1i[0] = volcoeffp * ov.sfp;
 
       // EV energy
       energy1i[0] = volcoeffp * ov.gamma1i * ov.volume;
       fenergy1i[0] = volcoeffp * ov.sfp * ov.gamma1i;
 
       // Loop over children.
       if (ov.childrenStartIndex >= 0) {
         for (int sloti = ov.childrenStartIndex;
              sloti < ov.childrenStartIndex + ov.childrenCount;
              sloti++) {
           double[] psi1it = new double[1];
           double[] f1it = new double[1];
           double[] p1it = new double[3];
           double[] psip1it = new double[1];
           double[] fp1it = new double[1];
           double[] pp1it = new double[3];
           double[] energy1it = new double[1];
           double[] fenergy1it = new double[1];
           double[] penergy1it = new double[3];
           computeVolumeUnderSlot2R(
               sloti,
               psi1it,
               f1it,
               p1it,
               psip1it,
               fp1it,
               pp1it,
               energy1it,
               fenergy1it,
               penergy1it,
               threadID,
               dr,
               dv,
               freeVolume,
               selfVolume);
           psi1i[0] += psi1it[0];
           f1i[0] += f1it[0];
           add(p1i, p1it, p1i);
 
           psip1i[0] += psip1it[0];
           fp1i[0] += fp1it[0];
           add(pp1i, pp1it, pp1i);
 
           energy1i[0] += energy1it[0];
           fenergy1i[0] += fenergy1it[0];
           add(penergy1i, penergy1it, penergy1i);
         }
       }
 
       // Skip this for the Root Level.
       if (ov.level > 0) {
         // Contributions to free and self volume of last atom
         freeVolume.add(threadID, atom, psi1i[0]);
         selfVolume.add(threadID, atom, psip1i[0]);
 
         // Contributions to energy gradients
         double c2 = ai / a1i;
 
         // dr[atom] += (-ov.dv1) * fenergy1i + penergy1i * c2;
         double[] work1 = new double[3];
         double[] work2 = new double[3];
         double[] work3 = new double[3];
         scale(penergy1i, c2, work1);
         scale(ov.dv1, -fenergy1i[0], work2);
         add(work1, work2, work3);
         dr.add(threadID, atom, work3[0], work3[1], work3[2]);
 
         // ov.g.v is the unswitched volume
         dv.add(threadID, atom, ov.g.v * fenergy1i[0]);
 
         // Update subtree P1..i's for parent
         c2 = a1 / a1i;
 
         // p1i = (ov.dv1) * f1i + p1i * c2;
         scale(ov.dv1, f1i[0], work1);
         scale(pp1i, c2, work2);
         add(work1, work2, p1i);
 
         // pp1i = (ov.dv1) * fp1i + pp1i * c2;
         scale(ov.dv1, fp1i[0], work1);
         scale(pp1i, c2, work2);
         add(work1, work2, pp1i);
 
         // penergy1i = (ov.dv1) * fenergy1i + penergy1i * c2;
         scale(ov.dv1, fenergy1i[0], work1);
         scale(penergy1i, c2, work2);
         add(work1, work2, penergy1i);
 
         // Update subtree F1..i's for parent
         f1i[0] = ov.dvv1 * f1i[0];
         fp1i[0] = ov.dvv1 * fp1i[0];
         fenergy1i[0] = ov.dvv1 * fenergy1i[0];
       }
     }
 
     /**
      * Recursively traverses tree and computes volumes, etc.
      *
      * @param volume     Volume.
      * @param energy     Energy.
      * @param dr         Coordinate derivatives.
      * @param dv         Volume derivatives.
      * @param freeVolume Free volume.
      * @param selfvolume Self volume.
      */
     void computeVolume2R(
         SharedDouble volume,
         SharedDouble energy,
         AtomicDoubleArray3D dr,
         AtomicDoubleArray dv,
         AtomicDoubleArray freeVolume,
         AtomicDoubleArray selfvolume) {
 
       double[] psi1i = new double[1];
       double[] f1i = new double[1];
       double[] p1i = new double[3];
       double[] psip1i = new double[1];
       double[] fp1i = new double[1];
       double[] pp1i = new double[3];
       double[] energy1i = new double[1];
       double[] fenergy1i = new double[1];
       double[] penergy1i = new double[3];
       // Only one thread for serial computation.
       int threadID = 0;
 
       computeVolumeUnderSlot2R(
           0,
           psi1i,
           f1i,
           p1i,
           psip1i,
           fp1i,
           pp1i,
           energy1i,
           fenergy1i,
           penergy1i,
           threadID,
           dr,
           dv,
           freeVolume,
           selfvolume);
 
       volume.addAndGet(psi1i[0]);
       energy.addAndGet(energy1i[0]);
     }
 
     /**
      * Rescan the tree to recompute the volumes. It does not modify the tree.
      *
      * @param pos        Atomic positions.
      * @param radii      Atomic radii.
      * @param volumes    Atomic volumes.
      * @param gammas     Atomic surface tensions.
      * @param ishydrogen True if the atom is a hydrogen.
      */
     void rescanTreeV(
         double[][] pos, double[] radii, double[] volumes, double[] gammas, boolean[] ishydrogen) {
       initRescanTreeV(pos, radii, volumes, gammas, ishydrogen);
       rescanR(0);
     }
 
     /**
      * Rescan the sub-tree to recompute the volumes. It does not modify the tree.
      *
      * @param slot The slot to begin from.
      */
     void rescanR(int slot) {
       int parentIndex;
 
       // This overlap.
       GaussianOverlap ov = overlaps.get(slot);
 
       // Recompute its own overlap by merging parent and last atom.
       parentIndex = ov.parentIndex;
       if (parentIndex > 0) {
         GaussianVca g12 = new GaussianVca();
         double[] dVdr = new double[1];
         double[] dVdV = new double[1];
         double[] sfp = new double[1];
 
         int atom = ov.atom;
         GaussianOverlap parent = overlaps.get(parentIndex);
         GaussianVca g1 = parent.g;
 
         // Atoms are stored in the tree at indexes 1...N
         GaussianVca g2 = overlaps.get(atom + 1).g;
         double gvol = overlapGaussianAlpha(g1, g2, g12, dVdr, dVdV, sfp);
         ov.g = g12;
         ov.volume = gvol;
 
         // dv1 is the gradient of V(123..)n with respect to the position of 1
         // ov.dv1 = ( g2.c - g1.c ) * (-dVdr);
         sub(g2.c, g1.c, ov.dv1);
         scale(ov.dv1, -dVdr[0], ov.dv1);
 
         // dvv1 is the derivative of V(123...)n with respect to V(123...)
         ov.dvv1 = dVdV[0];
         ov.sfp = sfp[0];
         ov.gamma1i = parent.gamma1i + overlaps.get(atom + 1).gamma1i;
       }
 
       // Calls itself recursively on the children.
       for (int slotChild = ov.childrenStartIndex;
            slotChild < ov.childrenStartIndex + ov.childrenCount;
            slotChild++) {
         rescanR(slotChild);
       }
     }
 
     /**
      * Init rescan of the tree to recompute the volumes. It does not modify the tree.
      *
      * @param pos        Atomic coodinates.
      * @param radii      Atomic radii.
      * @param volumes    Atomic volumes.
      * @param gammas     Atomic surface tensions.
      * @param ishydrogen True if the atom is a hydrogen.
      */
     void initRescanTreeV(
         double[][] pos, double[] radii, double[] volumes, double[] gammas, boolean[] ishydrogen) {
       int slot = 0;
       GaussianOverlap ov = overlaps.get(slot);
       ov.level = 0;
       ov.volume = 0.0;
       ov.dv1 = new double[3];
       ov.dvv1 = 0.0;
       ov.selfVolume = 0.0;
       ov.sfp = 1.0;
       ov.gamma1i = 0.0;
 
       slot = 1;
       for (int iat = 0; iat < nAtoms; iat++, slot++) {
         double a = sphereConversion / (radii[iat] * radii[iat]);
         double vol = ishydrogen[iat] ? 0.0 : volumes[iat];
         ov = overlaps.get(slot);
         ov.level = 1;
         ov.g.v = vol;
         ov.g.a = a;
         ov.g.c = pos[iat];
         ov.volume = vol;
         ov.dv1 = new double[3];
         ov.dvv1 = 1.0; // dVi/dVi
         ov.selfVolume = 0.0;
         ov.sfp = 1.0;
         ov.gamma1i = gammas[iat]; // gamma[iat]/SA_DR
       }
     }
 
     /**
      * Rescan the sub-tree to recompute the gammas. It does not modify the volumes nor the tree.
      *
      * @param slot Slot to begin from.
      */
     void rescanGammaR(int slot) {
 
       // This overlap.
       GaussianOverlap go = overlaps.get(slot);
 
       // Recompute its own overlap by merging parent and last atom.
       int parentIndex = go.parentIndex;
       if (parentIndex > 0) {
         int atom = go.atom;
         GaussianOverlap parent = overlaps.get(parentIndex);
         go.gamma1i = parent.gamma1i + overlaps.get(atom + 1).gamma1i;
       }
 
       // Calls itself recursively on the children.
       for (int slotChild = go.childrenStartIndex;
            slotChild < go.childrenStartIndex + go.childrenCount;
            slotChild++) {
         rescanGammaR(slotChild);
       }
     }
 
     /**
      * Rescan the tree to recompute the gammas only. It does not modify volumes and the tree.
      *
      * @param gammas Gamma values.
      */
     void rescanTreeG(double[] gammas) {
 
       int slot = 0;
       GaussianOverlap ov = overlaps.get(slot);
       ov.gamma1i = 0.;
 
       slot = 1;
       for (int iat = 0; iat < nAtoms; iat++, slot++) {
         ov = overlaps.get(slot);
         ov.gamma1i = gammas[iat];
       }
 
       rescanGammaR(0);
     }
 
     /**
      * Print the contents of the tree.
      */
     void printTree() {
       // logger.info("slot level LastAtom parent ChStart ChCount SelfV V gamma a x y z dedx dedy
       // dedz sfp");
       for (int i = 1; i <= nAtoms; i++) {
         printTreeR(i);
       }
     }
 
     /**
      * Print the contents of the tree (recursive).
      *
      * @param slot Slot to begin from.
      */
     void printTreeR(int slot) {
       GaussianOverlap ov = overlaps.get(slot);
       logger.info(format("tg:      %d ", slot));
       ov.printOverlap();
       for (int i = ov.childrenStartIndex; i < ov.childrenStartIndex + ov.childrenCount; i++) {
         printTreeR(i);
       }
     }
 
     /**
      * Counts number of overlaps under the one given.
      *
      * @param slot Slot to begin from.
      * @return Number of overlaps.
      */
     int nChildrenUnderSlotR(int slot) {
       int n = 0;
       if (overlaps.get(slot).childrenCount > 0) {
         n += overlaps.get(slot).childrenCount;
         // now calls itself on the children
         for (int i = 0; i < overlaps.get(slot).childrenCount; i++) {
           n += nChildrenUnderSlotR(overlaps.get(slot).childrenStartIndex + i);
         }
       }
       return n;
     }
   }
 
   /**
    * Use instances of the GaussianOverlapTree to compute the GaussVol volume in parallel.
    */
   private class GaussVolRegion extends ParallelRegion {
 
     private final InitGaussVol[] initGaussVol;
     private final GaussianOverlapTree[] localTree;
     private final ComputeTreeLoop[] computeTreeLoops;
     private final ComputeVolumeLoop[] computeVolumeLoops;
     private final RescanTreeLoop[] rescanTreeLoops;
     private final ReductionLoop[] reductionLoops;
     private GAUSSVOL_MODE mode = GAUSSVOL_MODE.COMPUTE_TREE;
     private double[][] coordinates = null;
 
     /**
      * GaussVolRegion constructor.
      *
      * @param nThreads Number of threads.
      */
     public GaussVolRegion(int nThreads) {
       initGaussVol = new InitGaussVol[nThreads];
       localTree = new GaussianOverlapTree[nThreads];
       computeTreeLoops = new ComputeTreeLoop[nThreads];
       computeVolumeLoops = new ComputeVolumeLoop[nThreads];
       rescanTreeLoops = new RescanTreeLoop[nThreads];
       reductionLoops = new ReductionLoop[nThreads];
     }
 
     public void init(GAUSSVOL_MODE mode, double[][] coordinates) {
       this.mode = mode;
       this.coordinates = coordinates;
 
       // Initialize output variables.
       totalVolume.set(0.0);
       energy.set(0.0);
       grad.reset(parallelTeam);
       gradV.reset(parallelTeam, 0, nAtoms - 1);
       freeVolume.reset(parallelTeam, 0, nAtoms - 1);
       selfVolume.reset(parallelTeam, 0, nAtoms - 1);
     }
 
     @Override
     public void run() throws Exception {
       int threadIndex = getThreadIndex();
       if (computeTreeLoops[threadIndex] == null) {
         initGaussVol[threadIndex] = new InitGaussVol();
         localTree[threadIndex] = new GaussianOverlapTree(nAtoms);
         computeTreeLoops[threadIndex] = new ComputeTreeLoop();
         computeVolumeLoops[threadIndex] = new ComputeVolumeLoop();
         rescanTreeLoops[threadIndex] = new RescanTreeLoop();
         reductionLoops[threadIndex] = new ReductionLoop();
       }
       try {
         if (mode == GAUSSVOL_MODE.COMPUTE_TREE) {
           execute(0, nAtoms - 1, initGaussVol[threadIndex]);
           execute(1, nAtoms, computeTreeLoops[threadIndex]);
           execute(1, nAtoms, computeVolumeLoops[threadIndex]);
           execute(0, nAtoms - 1, reductionLoops[threadIndex]);
         } else {
           execute(1, nAtoms, rescanTreeLoops[threadIndex]);
           execute(1, nAtoms, computeVolumeLoops[threadIndex]);
           execute(0, nAtoms - 1, reductionLoops[threadIndex]);
         }
       } catch (RuntimeException ex) {
         logger.warning("Runtime exception computing tree in thread: " + threadIndex);
         throw ex;
       } catch (Exception e) {
         String message = "Fatal exception computing tree in thread: " + threadIndex + "\n";
         logger.log(Level.SEVERE, message, e);
       }
     }
 
     private class InitGaussVol extends IntegerForLoop {
 
       @Override
       public void run(int first, int last) throws Exception {
         for (int i = first; i <= last; i++) {
           // Update the radius and volume for each atom.
           updateAtom(i);
         }
       }
     }
 
     /**
      * Initialize the Overlap tree for a subset of the system.
      */
     private class ComputeTreeLoop extends IntegerForLoop {
 
       @Override
       public void run(int first, int last) throws Exception {
         // Compute the overlaps for a subset of atoms.
         int threadIndex = getThreadIndex();
         for (int slot = first; slot <= last; slot++) {
           localTree[threadIndex].computeAndAddChildrenR(slot);
         }
       }
 
       @Override
       public void start() {
         localTree[getThreadIndex()].initOverlapTree(
             coordinates, radii, volumes, gammas, ishydrogen);
       }
     }
 
     /**
      * Compute the volume and derivatives for a subset of the system.
      */
     private class ComputeVolumeLoop extends IntegerForLoop {
 
       @Override
       public void run(int first, int last) throws Exception {
         int threadIndex = getThreadIndex();
         for (int slot = first; slot <= last; slot++) {
           double[] psi1i = new double[1];
           double[] f1i = new double[1];
           double[] p1i = new double[3];
           double[] psip1i = new double[1];
           double[] fp1i = new double[1];
           double[] pp1i = new double[3];
           double[] energy1i = new double[1];
           double[] fenergy1i = new double[1];
           double[] penergy1i = new double[3];
           localTree[threadIndex].computeVolumeUnderSlot2R(
               slot,
               psi1i,
               f1i,
               p1i,
               psip1i,
               fp1i,
               pp1i,
               energy1i,
               fenergy1i,
               penergy1i,
               threadIndex,
               grad,
               gradV,
               freeVolume,
               selfVolume);
           totalVolume.addAndGet(psi1i[0]);
           energy.addAndGet(energy1i[0]);
         }
       }
     }
 
     /**
      * Rescan the tree based on updated radii and volumes for a subset of the system.
      */
     private class RescanTreeLoop extends IntegerForLoop {
 
       @Override
       public void run(int first, int last) throws Exception {
         // Compute the overlaps for a subset of atoms.
         int threadIndex = getThreadIndex();
         for (int slot = first; slot <= last; slot++) {
           localTree[threadIndex].rescanR(slot);
         }
       }
 
       @Override
       public void start() {
         localTree[getThreadIndex()].initRescanTreeV(
             coordinates, radii, volumes, gammas, ishydrogen);
       }
     }
 
     /**
      * Reduce GaussVol gradient.
      */
     private class ReductionLoop extends IntegerForLoop {
 
       int threadID;
 
       @Override
       public void run(int lb, int ub) {
         grad.reduce(lb, ub);
         gradV.reduce(lb, ub);
         freeVolume.reduce(lb, ub);
         selfVolume.reduce(lb, ub);
         for (int i = lb; i <= ub; i++) {
           if (volumes[i] > 0) {
             gradV.set(0, i, gradV.get(i) / volumes[i]);
           }
         }
       }
 
       @Override
       public void start() {
         threadID = getThreadIndex();
       }
     }
   }
 }