// ******************************************************************************
   //
   // 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.nonbonded;
  
  import edu.rit.pj.IntegerForLoop;
  import edu.rit.pj.IntegerSchedule;
  import edu.rit.pj.ParallelRegion;
  import edu.rit.pj.ParallelTeam;
  import ffx.crystal.Crystal;
  import ffx.numerics.fft.Complex;
  import ffx.numerics.fft.Complex3DParallel;
  import ffx.potential.bonded.Atom;
  import ffx.potential.parameters.ForceField;
  import ffx.utilities.FFXProperty;
  import ffx.utilities.PropertyGroup;
  import org.apache.commons.configuration2.CompositeConfiguration;
  
  import java.nio.DoubleBuffer;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  import static ffx.numerics.fft.Complex3D.interleavedIndex;
  import static ffx.numerics.math.ScalarMath.mod;
  import static ffx.numerics.spline.UniformBSpline.bSpline;
  import static ffx.numerics.spline.UniformBSpline.bSplineDerivatives;
  import static ffx.potential.parameters.MultipoleType.t000;
  import static ffx.potential.parameters.MultipoleType.t001;
  import static ffx.potential.parameters.MultipoleType.t002;
  import static ffx.potential.parameters.MultipoleType.t003;
  import static ffx.potential.parameters.MultipoleType.t010;
  import static ffx.potential.parameters.MultipoleType.t011;
  import static ffx.potential.parameters.MultipoleType.t012;
  import static ffx.potential.parameters.MultipoleType.t020;
  import static ffx.potential.parameters.MultipoleType.t021;
  import static ffx.potential.parameters.MultipoleType.t030;
  import static ffx.potential.parameters.MultipoleType.t100;
  import static ffx.potential.parameters.MultipoleType.t101;
  import static ffx.potential.parameters.MultipoleType.t102;
  import static ffx.potential.parameters.MultipoleType.t110;
  import static ffx.potential.parameters.MultipoleType.t111;
  import static ffx.potential.parameters.MultipoleType.t120;
  import static ffx.potential.parameters.MultipoleType.t200;
  import static ffx.potential.parameters.MultipoleType.t201;
  import static ffx.potential.parameters.MultipoleType.t210;
  import static ffx.potential.parameters.MultipoleType.t300;
  import static java.lang.Math.fma;
  import static java.lang.String.format;
  import static java.lang.System.arraycopy;
  import static org.apache.commons.math3.util.FastMath.PI;
  import static org.apache.commons.math3.util.FastMath.cos;
  import static org.apache.commons.math3.util.FastMath.exp;
  import static org.apache.commons.math3.util.FastMath.floor;
  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.pow;
  import static org.apache.commons.math3.util.FastMath.round;
  import static org.apache.commons.math3.util.FastMath.sin;
  import static org.apache.commons.math3.util.FastMath.sqrt;
  
  /**
   * The Reciprocal Space class computes the reciprocal space contribution to {@link ParticleMeshEwald}
   * for the AMOEBA force field.
   *
   * <ol>
  *   <li>Assignment of polarizable multipole charge density to the 3D grid, via b-Splines, is
  *       parallelized using a spatial decomposition.
  *   <li>The convolution depends on methods of the {@link ffx.numerics.fft.Real3DParallel} and
  *       {@link ffx.numerics.fft.Complex3DParallel} classes.
  *   <li>Finally, the electric potential and its gradients are collected, in parallel, off the grid
  *       using b-Splines.
  * </ol>
  *
  * @author Michael J. Schnieders
  * @since 1.0
  */
 public class ReciprocalSpace {
 
   private static final Logger logger = Logger.getLogger(ReciprocalSpace.class.getName());
   /**
    * First lookup index to pack a 2D tensor into a 1D array.
    */
   private static final int[] qi1 = {0, 1, 2, 0, 0, 1};
   /**
    * Second lookup index to pack a 2D tensor into a 1D array.
    */
   private static final int[] qi2 = {0, 1, 2, 1, 2, 2};
 
   private static final double toSeconds = 1.0e-9;
   private final ParticleMeshEwald particleMeshEwald;
 
   private final ForceField.ELEC_FORM elecForm;
 
   private final ForceField forceField;
   /**
    * Number of unit cell symmetry operators.
    */
   private final int nSymm;
   /**
    * Number of threads.
    */
   private final int threadCount;
 
   /**
    * The default b-Spline order to use for discretization to/from the reciprocal grid.
    */
   private static final int DEFAULT_PME_ORDER = 5;
 
   /**
    * The b-Spline order to use for discretization to/from the reciprocal grid.
    */
   @FFXProperty(name = "pme-order", clazz = Integer.class, propertyGroup = PropertyGroup.ParticleMeshEwald,
       defaultValue = "5", description = """
       Sets the order of the B-spline interpolation used during particle mesh Ewald summation for partial charge
       or atomic multipole electrostatics. A default value of 5 is used in the absence of the pme-order keyword.
       """)
   private final int bSplineOrder;
   /**
    * Three derivatives of the potential are needed for AMOEBA. Specifically, the field gradient is
    * used to compute the energy of the quadrupole moment and the 2nd field gradient (3rd derivative
    * of the reciprocal potential) the energy gradient.
    */
   private final int derivOrder = 3;
   /**
    * The Ewald convergence parameter.
    */
   private final double aEwald;
   /**
    * Parallel team instance.
    */
   private final ParallelTeam parallelTeam;
   private final ParallelTeam fftTeam;
   private final BSplineRegion bSplineRegion;
   private final FractionalMultipoleRegion fractionalMultipoleRegion;
   private final FractionalInducedRegion fractionalInducedRegion;
   private final SpatialPermanentLoop[] spatialPermanentLoops;
   private final SpatialInducedLoop[] spatialInducedLoops;
   private final SlicePermanentLoop[] slicePermanentLoops;
   private final SliceInducedLoop[] sliceInducedLoops;
   private final RowPermanentLoop[] rowPermanentLoops;
   private final RowInducedLoop[] rowInducedLoops;
   /**
    * Number of atoms for a given symmetry operator that a given thread is responsible for applying to
    * the FFT grid. gridAtomCount[nSymm][nThread]
    */
   private final int[][] gridAtomCount;
   /**
    * Atom indices for a given symmetry operator that a given thread is responsible for applying to
    * the FFT grid. gridAtomCount[nSymm][nThread][nAtoms]
    */
   private final int[][][] gridAtomList;
   private final PermanentPhiRegion permanentPhiRegion;
   private final InducedPhiRegion polarizationPhiRegion;
   private final IntegerSchedule recipSchedule;
   /**
    * Convolution variables.
    */
   private final double[][] transformFieldMatrix = new double[10][10];
   private final double[][] transformMultipoleMatrix = new double[10][10];
   private final double[][] a = new double[3][3];
   private double[][][] inducedDipoleFrac;
   private double[][][] inducedDipoleFracCR;
   /**
    * The unit cell for the simulation. A ReplicatesCrystal will give equivalent results up to the
    * limits of double precision, but is more expensive.
    */
   private Crystal crystal;
   /**
    * Array of atoms in the asymmetric unit.
    */
   private Atom[] atoms;
   /**
    * Number of atoms in the asymmetric unit.
    */
   private int nAtoms;
 
   private static final double DEFAULT_PME_MESH_DENSITY = 1.2;
   private static final double oneThird = 1.0 / 3.0;
 
   @FFXProperty(name = "pme-mesh-density", clazz = Integer.class, propertyGroup = PropertyGroup.ParticleMeshEwald,
       defaultValue = "1.2", description = """
       The default in the absence of the pme-grid keyword is to set the grid size along each
       axis to the smallest factor of 2, 3 and/or 5 that is at least as large as
       pme-mesh-density times the axis length in Angstroms.
       """)
   private double density;
 
   /**
    * The X-dimension of the FFT grid.
    */
   @FFXProperty(name = "pme-grid-x", clazz = Integer.class, propertyGroup = PropertyGroup.ParticleMeshEwald,
       defaultValue = "NONE", description =
       "Specifies the PME grid dimension along the x-axis and takes precedence over the pme-grid keyword.")
   @FFXProperty(name = "pme-grid", clazz = Integer.class, propertyGroup = PropertyGroup.ParticleMeshEwald,
       defaultValue = "NONE", description = """
       [3 integers]
       Sets the dimensions of the reciprocal space grid used during particle mesh Ewald
       summation for electrostatics. The three modifiers give the size along the X-, Y- and Z- axes,
       respectively. If either the Y- or Z-axis dimensions are omitted, then they are set equal
       to the X-axis dimension. The default in the absence of the pme-grid keyword is to set the
       grid size along each axis to the smallest value that can be factored by 2, 3, 4 and/or 5
       and is at least as large as 1.2 times the axis length in Angstroms.
       The value 1.2 can be changed using the pme-mesh-density property.
       """)
   private int fftX;
 
   /**
    * The Y-dimension of the FFT grid.
    */
   @FFXProperty(name = "pme-grid-y", clazz = Integer.class, propertyGroup = PropertyGroup.ParticleMeshEwald,
       defaultValue = "NONE", description =
       "Specifies the PME grid dimension along the y-axis and takes precedence over the pme-grid keyword.")
   private int fftY;
 
   /**
    * The Z-dimension of the FFT grid.
    */
   @FFXProperty(name = "pme-grid-z", clazz = Integer.class, propertyGroup = PropertyGroup.ParticleMeshEwald,
       defaultValue = "NONE", description =
       "Specifies the PME grid dimension along the z-axis and takes precedence over the pme-grid keyword.")
   private int fftZ;
 
   /**
    * Number of doubles needed to compute a complex to complex 3D FFT (fftX * fftY * fftZ * 2).
    */
   private int fftSpace;
   /**
    * Reciprocal space grid. [fftSpace]
    */
   private double[] splineGrid;
   /**
    * Wraps the splineGrid.
    */
   private DoubleBuffer splineBuffer;
   /**
    * Reference to atomic coordinate array.
    */
   private double[][][] coordinates;
   // Spline moments and perform the convolution.
   private SpatialDensityRegion spatialDensityRegion;
   private SliceRegion sliceRegion;
   private RowRegion rowRegion;
   private Complex3DParallel complex3DFFT;
   private GridMethod gridMethod;
   // Timing variables.
   private long bSplineTotal, splinePermanentTotal, splineInducedTotal;
   private long permanentPhiTotal, inducedPhiTotal, convTotal;
   /**
    * Timing variables.
    */
   private final long[] bSplineTime;
   private final long[] splinePermanentTime;
   private final long[] permanentPhiTime;
   private final long[] splineInducedTime;
   private final int[] splineCount;
   private final long[] inducedPhiTime;
 
 
   /**
    * Reciprocal Space PME contribution.
    *
    * @param particleMeshEwald a {@link ParticleMeshEwald} object.
    * @param crystal           a {@link ffx.crystal.Crystal} object.
    * @param forceField        a {@link ffx.potential.parameters.ForceField} object.
    * @param atoms             an array of {@link ffx.potential.bonded.Atom} objects.
    * @param aewald            the Ewald parameter.
    * @param fftTeam           a {@link edu.rit.pj.ParallelTeam} object.
    * @param parallelTeam      a {@link edu.rit.pj.ParallelTeam} object.
    */
   public ReciprocalSpace(
       ParticleMeshEwald particleMeshEwald,
       Crystal crystal,
       ForceField forceField,
       Atom[] atoms,
       double aewald,
       ParallelTeam fftTeam,
       ParallelTeam parallelTeam) {
 
     this.particleMeshEwald = particleMeshEwald;
     this.crystal = crystal.getUnitCell();
     this.forceField = forceField;
     this.atoms = atoms;
     this.nAtoms = atoms.length;
     this.aEwald = aewald;
     this.fftTeam = fftTeam;
     this.parallelTeam = parallelTeam;
     this.elecForm = particleMeshEwald.getElecForm();
 
     coordinates = particleMeshEwald.getCoordinates();
     threadCount = parallelTeam.getThreadCount();
     nSymm = this.crystal.spaceGroup.getNumberOfSymOps();
 
     // Construct the parallel convolution object.
     boolean available;
     String recipStrategy = null;
     try {
       recipStrategy = forceField.getString("RECIP_SCHEDULE");
       IntegerSchedule.parse(recipStrategy);
       available = true;
     } catch (Exception e) {
       available = false;
     }
     if (available) {
       recipSchedule = IntegerSchedule.parse(recipStrategy);
       logger.log(Level.INFO, "  Convolution schedule {0}", recipStrategy);
     } else {
       recipSchedule = IntegerSchedule.fixed();
     }
 
     CompositeConfiguration properties = forceField.getProperties();
     String gridString = properties.getString("grid-method", "SPATIAL").toUpperCase();
     try {
       gridMethod = GridMethod.valueOf(gridString);
     } catch (Exception e) {
       gridMethod = GridMethod.SPATIAL;
     }
 
     bSplineOrder = forceField.getInteger("PME_ORDER", DEFAULT_PME_ORDER);
 
     // Initialize convolution objects that may be re-allocated during NPT simulations.
     double density = initConvolution();
 
     // Log PME reciprocal space parameters.
     if (logger.isLoggable(Level.INFO)) {
       StringBuilder sb = new StringBuilder();
       sb.append(format("    B-Spline Order:                    %8d\n", bSplineOrder));
       sb.append(format("    Mesh Density:                      %8.3f\n", density));
       sb.append(format("    Mesh Dimensions:              (%3d,%3d,%3d)\n", fftX, fftY, fftZ));
       sb.append(format("    Grid Method:                       %8s\n", gridMethod.toString()));
       logger.info(sb.toString());
     }
 
     // Construct the parallel BSplineRegion, DensityLoops and Phi objects.
     bSplineRegion = new BSplineRegion();
     fractionalMultipoleRegion = new FractionalMultipoleRegion();
     fractionalInducedRegion = new FractionalInducedRegion();
     switch (gridMethod) {
       default -> {
         spatialPermanentLoops = new SpatialPermanentLoop[threadCount];
         spatialInducedLoops = new SpatialInducedLoop[threadCount];
         for (int i = 0; i < threadCount; i++) {
           spatialPermanentLoops[i] = new SpatialPermanentLoop(spatialDensityRegion, bSplineRegion);
           spatialInducedLoops[i] = new SpatialInducedLoop(spatialDensityRegion, bSplineRegion);
         }
         slicePermanentLoops = null;
         sliceInducedLoops = null;
         rowPermanentLoops = null;
         rowInducedLoops = null;
         gridAtomCount = null;
         gridAtomList = null;
       }
       case ROW -> {
         rowPermanentLoops = new RowPermanentLoop[threadCount];
         rowInducedLoops = new RowInducedLoop[threadCount];
         for (int i = 0; i < threadCount; i++) {
           rowPermanentLoops[i] = new RowPermanentLoop(rowRegion, bSplineRegion);
           rowInducedLoops[i] = new RowInducedLoop(rowRegion, bSplineRegion);
         }
         gridAtomCount = new int[nSymm][threadCount];
         gridAtomList = new int[nSymm][threadCount][nAtoms];
         spatialPermanentLoops = null;
         spatialInducedLoops = null;
         slicePermanentLoops = null;
         sliceInducedLoops = null;
       }
       case SLICE -> {
         slicePermanentLoops = new SlicePermanentLoop[threadCount];
         sliceInducedLoops = new SliceInducedLoop[threadCount];
         for (int i = 0; i < threadCount; i++) {
           slicePermanentLoops[i] = new SlicePermanentLoop(sliceRegion, bSplineRegion);
           sliceInducedLoops[i] = new SliceInducedLoop(sliceRegion, bSplineRegion);
         }
         gridAtomCount = new int[nSymm][threadCount];
         gridAtomList = new int[nSymm][threadCount][nAtoms];
         spatialPermanentLoops = null;
         spatialInducedLoops = null;
         rowPermanentLoops = null;
         rowInducedLoops = null;
       }
     }
     permanentPhiRegion = new PermanentPhiRegion(bSplineRegion);
     polarizationPhiRegion = new InducedPhiRegion(bSplineRegion);
 
     // Initialize timing variables.
     bSplineTime = new long[threadCount];
     splinePermanentTime = new long[threadCount];
     splineInducedTime = new long[threadCount];
     splineCount = new int[threadCount];
     permanentPhiTime = new long[threadCount];
     inducedPhiTime = new long[threadCount];
   }
 
   /**
    * Computes the modulus of the discrete Fourier Transform of "bsarray" and stores it in "bsmod".
    *
    * @param bsmod   B-Spline modulus.
    * @param bsarray B-Spline array.
    * @param nfft    FFT dimension.
    * @param order   B-Spline order.
    */
   private static void discreteFTMod(double[] bsmod, double[] bsarray, int nfft, int order) {
     // Get the modulus of the discrete Fourier fft.
     double factor = 2.0 * PI / nfft;
     for (int i = 0; i < nfft; i++) {
       double sum1 = 0.0;
       double sum2 = 0.0;
       for (int j = 0; j < nfft; j++) {
         double arg = factor * (i * j);
         sum1 = sum1 + bsarray[j] * cos(arg);
         sum2 = sum2 + bsarray[j] * sin(arg);
       }
       bsmod[i] = sum1 * sum1 + sum2 * sum2;
     }
 
     // Fix for exponential Euler spline interpolation failure.
     double eps = 1.0e-7;
     if (bsmod[0] < eps) {
       bsmod[0] = 0.5 * bsmod[1];
     }
     for (int i = 1; i < nfft - 1; i++) {
       if (bsmod[i] < eps) {
         bsmod[i] = 0.5 * (bsmod[i - 1] + bsmod[i + 1]);
       }
     }
     if (bsmod[nfft - 1] < eps) {
       bsmod[nfft - 1] = 0.5 * bsmod[nfft - 2];
     }
 
     // Compute and apply the optimal zeta coefficient.
     int jcut = 50;
     int order2 = 2 * order;
     for (int i = 0; i < nfft; i++) {
       int k = i;
       double zeta;
       if (i > nfft / 2) {
         k = k - nfft;
       }
       if (k == 0) {
         zeta = 1.0;
       } else {
         double sum1 = 1.0;
         double sum2 = 1.0;
         factor = PI * k / nfft;
         for (int j = 0; j < jcut; j++) {
           double arg = factor / (factor + PI * (j + 1));
           sum1 = sum1 + pow(arg, order);
           sum2 = sum2 + pow(arg, order2);
         }
         for (int j = 0; j < jcut; j++) {
           double arg = factor / (factor - PI * (j + 1));
           sum1 = sum1 + pow(arg, order);
           sum2 = sum2 + pow(arg, order2);
         }
         zeta = sum2 / sum1;
       }
       bsmod[i] = bsmod[i] * zeta * zeta;
     }
   }
 
   /**
    * cartToFracInducedDipoles
    *
    * @param inducedDipole       Input Cartesian induced dipole.
    * @param inducedDipoleCR     Input Cartesian induced dipole CR.
    * @param fracInducedDipole   Output fractional induced dipole.
    * @param fracInducedDipoleCR Output fractional induced dipole CR.
    */
   public void cartToFracInducedDipole(
       double[] inducedDipole,
       double[] inducedDipoleCR,
       double[] fracInducedDipole,
       double[] fracInducedDipoleCR) {
     double[] in = inducedDipole;
     fracInducedDipole[0] = a[0][0] * in[0] + a[0][1] * in[1] + a[0][2] * in[2];
     fracInducedDipole[1] = a[1][0] * in[0] + a[1][1] * in[1] + a[1][2] * in[2];
     fracInducedDipole[2] = a[2][0] * in[0] + a[2][1] * in[1] + a[2][2] * in[2];
     in = inducedDipoleCR;
     fracInducedDipoleCR[0] = a[0][0] * in[0] + a[0][1] * in[1] + a[0][2] * in[2];
     fracInducedDipoleCR[1] = a[1][0] * in[0] + a[1][1] * in[1] + a[1][2] * in[2];
     fracInducedDipoleCR[2] = a[2][0] * in[0] + a[2][1] * in[1] + a[2][2] * in[2];
   }
 
   /**
    * computeBSplines
    */
   public void computeBSplines() {
     try {
       bSplineTotal -= System.nanoTime();
       parallelTeam.execute(bSplineRegion);
       bSplineTotal += System.nanoTime();
     } catch (Exception e) {
       String message = " Fatal exception evaluating b-Splines.";
       logger.log(Level.SEVERE, message, e);
     }
   }
 
   /**
    * computeInducedPhi
    *
    * @param cartInducedDipolePhi   an array of double.
    * @param cartInducedDipoleCRPhi an array of double.
    * @param fracInducedDipolePhi   an array of double.
    * @param fracInducedDipoleCRPhi an array of double.
    */
   public void computeInducedPhi(
       double[][] cartInducedDipolePhi, double[][] cartInducedDipoleCRPhi,
       double[][] fracInducedDipolePhi, double[][] fracInducedDipoleCRPhi) {
     inducedPhiTotal -= System.nanoTime();
     try {
       polarizationPhiRegion.setInducedDipolePhi(
           cartInducedDipolePhi, cartInducedDipoleCRPhi,
           fracInducedDipolePhi, fracInducedDipoleCRPhi);
       parallelTeam.execute(polarizationPhiRegion);
     } catch (Exception e) {
       String message = "Fatal exception evaluating induced reciprocal space potential.";
       logger.log(Level.SEVERE, message, e);
     }
     inducedPhiTotal += System.nanoTime();
   }
 
   /**
    * Compute the potential Phi and its derivatives for all atoms.
    *
    * @param cartPermanentPhi an array of double.
    * @param fracPermanentPhi an array of double.
    */
   public void computePermanentPhi(double[][] cartPermanentPhi, double[][] fracPermanentPhi) {
     permanentPhiTotal -= System.nanoTime();
     try {
       permanentPhiRegion.setPermanentPhi(cartPermanentPhi, fracPermanentPhi);
       parallelTeam.execute(permanentPhiRegion);
     } catch (Exception e) {
       String message = " Fatal exception evaluating permanent reciprocal space potential.";
       logger.log(Level.SEVERE, message, e);
     }
     permanentPhiTotal += System.nanoTime();
   }
 
   /**
    * getXDim
    *
    * @return the X dimension of the FFT grid.
    */
   public int getXDim() {
     return fftX;
   }
 
   /**
    * getYDim
    *
    * @return the Y dimension of the FFT grid.
    */
   public int getYDim() {
     return fftY;
   }
 
   /**
    * getZDim
    *
    * @return the Z dimension of the FFT grid.
    */
   public int getZDim() {
     return fftZ;
   }
 
   /**
    * Compute the reciprocal space field using a convolution.
    */
   public void performConvolution() {
     convTotal -= System.nanoTime();
     try {
       complex3DFFT.convolution(splineGrid);
     } catch (Exception e) {
       String message = "Fatal exception evaluating the convolution.";
       logger.log(Level.SEVERE, message, e);
     }
     convTotal += System.nanoTime();
   }
 
   /**
    * initTimings.
    */
   public void initTimings() {
     // Reset total timings.
     bSplineTotal = 0;
     splinePermanentTotal = 0;
     splineInducedTotal = 0;
     permanentPhiTotal = 0;
     inducedPhiTotal = 0;
     convTotal = 0;
 
     // Reset timing arrays.
     for (int i = 0; i < threadCount; i++) {
       bSplineTime[i] = 0;
       splinePermanentTime[i] = 0;
       splineInducedTime[i] = 0;
       permanentPhiTime[i] = 0;
       inducedPhiTime[i] = 0;
       splineCount[i] = 0;
     }
 
     // Reset 3D convolution timing.
     if (complex3DFFT != null) {
       complex3DFFT.initTiming();
     }
   }
 
   /**
    * printTimings.
    */
   public void printTimings() {
     if (logger.isLoggable(Level.FINE)) {
       if (complex3DFFT != null) {
         double total = (bSplineTotal + convTotal
             + splinePermanentTotal + permanentPhiTotal
             + splineInducedTotal + inducedPhiTotal) * toSeconds;
 
         logger.fine(format("\n Reciprocal Space: %7.4f (sec)", total));
         long[] convTime = complex3DFFT.getTiming();
         logger.fine("                           Direct Field    SCF Field");
         logger.fine(" Thread  B-Spline  3DConv  Spline  Phi     Spline  Phi      Count");
 
         long minBSpline = Long.MAX_VALUE;
         long maxBSpline = 0;
         long minConv = Long.MAX_VALUE;
         long maxConv = 0;
         long minBSPerm = Long.MAX_VALUE;
         long maxBSPerm = 0;
         long minPhiPerm = Long.MAX_VALUE;
         long maxPhiPerm = 0;
         long minBSInduced = Long.MAX_VALUE;
         long maxBSInduced = 0;
         long minPhiInduced = Long.MAX_VALUE;
         long maxPhiInduced = 0;
         int minCount = Integer.MAX_VALUE;
         int maxCount = 0;
 
         for (int i = 0; i < threadCount; i++) {
           logger.fine(format("    %3d   %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f  %6d",
               i, bSplineTime[i] * toSeconds, convTime[i] * toSeconds,
               splinePermanentTime[i] * toSeconds, permanentPhiTime[i] * toSeconds,
               splineInducedTime[i] * toSeconds, inducedPhiTime[i] * toSeconds,
               splineCount[i]));
           minBSpline = min(bSplineTime[i], minBSpline);
           maxBSpline = max(bSplineTime[i], maxBSpline);
           minConv = min(convTime[i], minConv);
           maxConv = max(convTime[i], maxConv);
           minBSPerm = min(splinePermanentTime[i], minBSPerm);
           maxBSPerm = max(splinePermanentTime[i], maxBSPerm);
           minPhiPerm = min(permanentPhiTime[i], minPhiPerm);
           maxPhiPerm = max(permanentPhiTime[i], maxPhiPerm);
           minBSInduced = min(splineInducedTime[i], minBSInduced);
           maxBSInduced = max(splineInducedTime[i], maxBSInduced);
           minPhiInduced = min(inducedPhiTime[i], minPhiInduced);
           maxPhiInduced = max(inducedPhiTime[i], maxPhiInduced);
           minCount = min(splineCount[i], minCount);
           maxCount = max(splineCount[i], maxCount);
         }
         logger.fine(format(" Min      %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f  %6d",
             minBSpline * toSeconds, minConv * toSeconds,
             minBSPerm * toSeconds, minPhiPerm * toSeconds,
             minBSInduced * toSeconds, minPhiInduced * toSeconds,
             minCount));
         logger.fine(format(" Max      %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f  %6d",
             maxBSpline * toSeconds, maxConv * toSeconds,
             maxBSPerm * toSeconds, maxPhiPerm * toSeconds,
             maxBSInduced * toSeconds, maxPhiInduced * toSeconds,
             maxCount));
         logger.fine(format(" Delta    %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f  %6d",
             (maxBSpline - minBSpline) * toSeconds,
             (maxConv - minConv) * toSeconds,
             (maxBSPerm - minBSPerm) * toSeconds,
             (maxPhiPerm - minPhiPerm) * toSeconds,
             (maxBSInduced - minBSInduced) * toSeconds,
             (maxPhiInduced - minPhiInduced) * toSeconds,
             (maxCount - minCount)));
         logger.fine(format(" Actual   %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f  %6d",
             bSplineTotal * toSeconds, convTotal * toSeconds,
             splinePermanentTotal * toSeconds, permanentPhiTotal * toSeconds,
             splineInducedTotal * toSeconds, inducedPhiTotal * toSeconds,
             nAtoms * nSymm));
       }
     }
   }
 
   /**
    * Setter for the field <code>atoms</code>.
    *
    * @param atoms an array of {@link ffx.potential.bonded.Atom} objects.
    */
   public void setAtoms(Atom[] atoms) {
     this.atoms = atoms;
     nAtoms = atoms.length;
     coordinates = particleMeshEwald.getCoordinates();
     switch (gridMethod) {
       case SPATIAL -> {
         spatialDensityRegion.setAtoms(atoms);
         spatialDensityRegion.coordinates = coordinates;
       }
       case ROW -> {
         rowRegion.setAtoms(atoms);
         rowRegion.coordinates = coordinates;
       }
       case SLICE -> {
         sliceRegion.setAtoms(atoms);
         sliceRegion.coordinates = coordinates;
       }
     }
   }
 
   /**
    * Setter for the field <code>crystal</code>.
    *
    * @param crystal a {@link ffx.crystal.Crystal} object.
    */
   public void setCrystal(Crystal crystal) {
     // Check if the number of symmetry operators has changed.
     this.crystal = crystal.getUnitCell();
     if (nSymm != this.crystal.spaceGroup.getNumberOfSymOps()) {
       logger.info(this.crystal.toString());
       logger.info(crystal.toString());
       logger.severe(
           " The reciprocal space class does not currently allow changes in the number of symmetry operators unless it is mapped by a user supplied symmetry operator.");
     }
     this.coordinates = particleMeshEwald.getCoordinates();
     initConvolution();
   }
 
   /**
    * Place the induced dipoles onto the FFT grid for the atoms in use.
    *
    * @param inducedDipole   Induced dipoles.
    * @param inducedDipoleCR Chain rule term for induced dipole gradient.
    * @param use             The atoms in use.
    */
   public void splineInducedDipoles(
       double[][][] inducedDipole, double[][][] inducedDipoleCR, boolean[] use) {
     splineInducedTotal -= System.nanoTime();
 
     try {
       // Allocate memory if needed.
       if (inducedDipoleFrac == null ||
           inducedDipoleFrac.length != inducedDipole.length ||
           inducedDipoleFrac[0].length != inducedDipole[0].length) {
         int nAtoms = inducedDipole.length;
         int nSymm = inducedDipole[0].length;
         inducedDipoleFrac = new double[nAtoms][nSymm][3];
         inducedDipoleFracCR = new double[nAtoms][nSymm][3];
       }
       // Compute fractional induced dipoles.
       fractionalInducedRegion.setUse(use);
       fractionalInducedRegion.setInducedDipoles(inducedDipole, inducedDipoleCR,
           inducedDipoleFrac, inducedDipoleFracCR);
       parallelTeam.execute(fractionalInducedRegion);
     } catch (Exception e) {
       String message = " Fatal exception evaluating fractional induced dipoles.";
       logger.log(Level.SEVERE, message, e);
     }
 
     switch (gridMethod) {
       case SPATIAL -> {
         spatialDensityRegion.setDensityLoop(spatialInducedLoops);
         for (int i = 0; i < threadCount; i++) {
           spatialInducedLoops[i].setInducedDipoles(inducedDipoleFrac, inducedDipoleFracCR);
           spatialInducedLoops[i].setUse(use);
           spatialInducedLoops[i].setRegion(spatialDensityRegion);
         }
         try {
           parallelTeam.execute(spatialDensityRegion);
         } catch (Exception e) {
           String message = " Fatal exception evaluating induced density.\n";
           logger.log(Level.SEVERE, message, e);
         }
       }
       case ROW -> {
         rowRegion.setDensityLoop(rowInducedLoops);
         for (int i = 0; i < threadCount; i++) {
           rowInducedLoops[i].setInducedDipoles(inducedDipoleFrac, inducedDipoleFracCR);
           rowInducedLoops[i].setUse(use);
         }
         try {
           parallelTeam.execute(rowRegion);
         } catch (Exception e) {
           String message = " Fatal exception evaluating induced density.";
           logger.log(Level.SEVERE, message, e);
         }
       }
       default -> {
         sliceRegion.setDensityLoop(sliceInducedLoops);
         for (int i = 0; i < threadCount; i++) {
           sliceInducedLoops[i].setInducedDipoles(inducedDipoleFrac, inducedDipoleFracCR);
           sliceInducedLoops[i].setUse(use);
         }
         try {
           parallelTeam.execute(sliceRegion);
         } catch (Exception e) {
           String message = " Fatal exception evaluating induced density.";
           logger.log(Level.SEVERE, message, e);
         }
       }
     }
     splineInducedTotal += System.nanoTime();
   }
 
   /**
    * Use b-Splines to place the permanent multipoles onto the FFT grid for the atoms in use.
    *
    * @param globalMultipoles an array of double.
    * @param fracMultipoles   an array of double.
    * @param use              an array of boolean.
    */
   public void splinePermanentMultipoles(double[][][] globalMultipoles, double[][][] fracMultipoles,
                                         boolean[] use) {
     splinePermanentTotal -= System.nanoTime();
 
     try {
       fractionalMultipoleRegion.setUse(use);
       fractionalMultipoleRegion.setPermanent(globalMultipoles, fracMultipoles);
       parallelTeam.execute(fractionalMultipoleRegion);
     } catch (Exception e) {
       String message = " Fatal exception evaluating fractional multipoles.";
       logger.log(Level.SEVERE, message, e);
     }
 
     switch (gridMethod) {
       case SPATIAL -> {
         spatialDensityRegion.setCrystal(crystal.getUnitCell(), fftX, fftY, fftZ);
         spatialDensityRegion.assignAtomsToCells();
         spatialDensityRegion.setDensityLoop(spatialPermanentLoops);
         for (int i = 0; i < threadCount; i++) {
           spatialPermanentLoops[i].setPermanent(fracMultipoles);
           spatialPermanentLoops[i].setUse(use);
           spatialPermanentLoops[i].setRegion(spatialDensityRegion);
         }
         try {
           parallelTeam.execute(spatialDensityRegion);
         } catch (Exception e) {
           String message = " Fatal exception evaluating permanent multipole density.";
           logger.log(Level.SEVERE, message, e);
         }
       }
       case ROW -> {
         rowRegion.setCrystal(crystal.getUnitCell(), fftX, fftY, fftZ);
         rowRegion.setDensityLoop(rowPermanentLoops);
         for (int i = 0; i < threadCount; i++) {
           rowPermanentLoops[i].setPermanent(fracMultipoles);
           rowPermanentLoops[i].setUse(use);
         }
         try {
           parallelTeam.execute(rowRegion);
         } catch (Exception e) {
           String message = " Fatal exception evaluating permanent multipole density.";
           logger.log(Level.SEVERE, message, e);
         }
       }
       case SLICE -> {
         sliceRegion.setCrystal(crystal.getUnitCell(), fftX, fftY, fftZ);
         sliceRegion.setDensityLoop(slicePermanentLoops);
         for (int i = 0; i < threadCount; i++) {
           slicePermanentLoops[i].setPermanent(fracMultipoles);
           slicePermanentLoops[i].setUse(use);
         }
         try {
           parallelTeam.execute(sliceRegion);
         } catch (Exception e) {
           String message = " Fatal exception evaluating permanent multipole density.";
           logger.log(Level.SEVERE, message, e);
         }
       }
     }
 
     splinePermanentTotal += System.nanoTime();
   }
 
   private double initConvolution() {
 
     // Store the current reciprocal space grid dimensions.
     int fftXCurrent = fftX;
     int fftYCurrent = fftY;
     int fftZCurrent = fftZ;
 
     // Support the PME-GRID keyword.
     int defaultX = -1;
     int defaultY = -1;
     int defaultZ = -1;
     if (forceField.hasProperty("PME_GRID")) {
       String grid = forceField.getString("PME_GRID", "-1 -1 -1");
       String[] values = grid.trim().split(" +");
       if (values != null) {
         defaultX = Integer.parseInt(values[0]);
         defaultY = defaultX;
         defaultZ = defaultX;
         if (values.length > 1) {
           defaultY = Integer.parseInt(values[1]);
           if (values.length > 2) {
             defaultZ = Integer.parseInt(values[2]);
           }
         }
       }
     }
 
     density = forceField.getDouble("PME_MESH_DENSITY", DEFAULT_PME_MESH_DENSITY);
 
     int nX = forceField.getInteger("PME_GRID_X", defaultX);
     if (nX < 2) {
       nX = (int) floor(crystal.a * density) + 1;
       if (nX % 2 != 0) {
         nX += 1;
       }
       while (!Complex.preferredDimension(nX)) {
         nX += 2;
       }
     }
 
     int nY = forceField.getInteger("PME_GRID_Y", defaultY);
     if (nY < 2) {
       nY = (int) floor(crystal.b * density) + 1;
       if (nY % 2 != 0) {
         nY += 1;
       }
       while (!Complex.preferredDimension(nY)) {
         nY += 2;
       }
     }
 
     int nZ = forceField.getInteger("PME_GRID_Z", defaultZ);
     if (nZ < 2) {
       nZ = (int) floor(crystal.c * density) + 1;
       if (nZ % 2 != 0) {
         nZ += 1;
       }
       while (!Complex.preferredDimension(nZ)) {
         nZ += 2;
       }
     }
 
     int minGrid = forceField.getInteger("PME_GRID_MIN", 16);
     nX = max(nX, minGrid);
     nY = max(nY, minGrid);
     nZ = max(nZ, minGrid);
 
     fftX = nX;
     fftY = nY;
     fftZ = nZ;
 
     // Populate the matrix that fractionalizes multipoles.
     transformMultipoleMatrix();
 
     // Populate the matrix that convert fractional potential components into orthogonal Cartesian
     // coordinates.
     transformFieldMatrix();
 
     // Compute the Cartesian to fractional matrix.
     for (int i = 0; i < 3; i++) {
       a[0][i] = fftX * crystal.A[i][0];
       a[1][i] = fftY * crystal.A[i][1];
       a[2][i] = fftZ * crystal.A[i][2];
     }
 
     fftSpace = fftX * fftY * fftZ * 2;
     boolean dimChanged = fftX != fftXCurrent || fftY != fftYCurrent || fftZ != fftZCurrent;
 
     if (complex3DFFT == null || dimChanged) {
       complex3DFFT = new Complex3DParallel(fftX, fftY, fftZ, fftTeam, recipSchedule);
       if (splineGrid == null || splineGrid.length < fftSpace) {
         splineGrid = new double[fftSpace];
       }
       splineBuffer = DoubleBuffer.wrap(splineGrid);
     }
     complex3DFFT.setRecip(generalizedInfluenceFunction());
 
     switch (gridMethod) {
       case SPATIAL -> {
         if (spatialDensityRegion == null || dimChanged) {
           spatialDensityRegion = new SpatialDensityRegion(fftX, fftY, fftZ, splineGrid, bSplineOrder,
               nSymm, 10, threadCount, crystal, atoms, coordinates);
         } else {
           spatialDensityRegion.setCrystal(crystal, fftX, fftY, fftZ);
           spatialDensityRegion.coordinates = coordinates;
         }
       }
       case ROW -> {
         if (rowRegion == null || dimChanged) {
           rowRegion = new RowRegion(fftX, fftY, fftZ, splineGrid, nSymm, threadCount, atoms, coordinates);
         } else {
           rowRegion.setCrystal(crystal, fftX, fftY, fftZ);
           rowRegion.coordinates = coordinates;
         }
       }
       case SLICE -> {
         if (sliceRegion == null || dimChanged) {
           sliceRegion = new SliceRegion(fftX, fftY, fftZ, splineGrid, nSymm, threadCount, atoms, coordinates);
         } else {
           sliceRegion.setCrystal(crystal, fftX, fftY, fftZ);
           sliceRegion.coordinates = coordinates;
         }
       }
     }
 
     return density;
   }
 
   private int RowIndexZ(int i) {
     return i / fftY;
   }
 
   private int RowIndexY(int i) {
     return i % fftY;
   }
 
   private double[] generalizedInfluenceFunction() {
 
     double[] influenceFunction = new double[fftSpace / 2];
 
     double[] bsModX = new double[fftX];
     double[] bsModY = new double[fftY];
     double[] bsModZ = new double[fftZ];
     int maxfft = max(max(max(fftX, fftY), fftZ), bSplineOrder + 1);
     double[] bsArray = new double[maxfft];
     double[] c = new double[bSplineOrder];
 
     bSpline(0.0, bSplineOrder, c);
     arraycopy(c, 0, bsArray, 1, bSplineOrder);
 
     discreteFTMod(bsModX, bsArray, fftX, bSplineOrder);
     discreteFTMod(bsModY, bsArray, fftY, bSplineOrder);
     discreteFTMod(bsModZ, bsArray, fftZ, bSplineOrder);
 
     double r00 = crystal.A[0][0];
     double r01 = crystal.A[0][1];
     double r02 = crystal.A[0][2];
     double r10 = crystal.A[1][0];
     double r11 = crystal.A[1][1];
     double r12 = crystal.A[1][2];
     double r20 = crystal.A[2][0];
     double r21 = crystal.A[2][1];
     double r22 = crystal.A[2][2];
     int ntot = fftX * fftY * fftZ;
     double piTerm = (PI / aEwald) * (PI / aEwald);
     double volTerm = PI * crystal.volume;
     int nfXY = fftX * fftY;
     int nX_2 = (fftX + 1) / 2;
     int nY_2 = (fftY + 1) / 2;
     int nZ_2 = (fftZ + 1) / 2;
 
     for (int i = 0; i < ntot - 1; i++) {
       int kZ = (i + 1) / nfXY;
       int j = i - kZ * nfXY + 1;
       int kY = j / fftX;
       int kX = j - kY * fftX;
       int h = kX;
       int k = kY;
       int l = kZ;
       if (kX >= nX_2) {
         h -= fftX;
       }
       if (kY >= nY_2) {
         k -= fftY;
       }
       if (kZ >= nZ_2) {
         l -= fftZ;
       }
       double sX = r00 * h + r01 * k + r02 * l;
       double sY = r10 * h + r11 * k + r12 * l;
       double sZ = r20 * h + r21 * k + r22 * l;
       double sSquared = sX * sX + sY * sY + sZ * sZ;
       double term = -piTerm * sSquared;
       double expterm = 0.0;
       if (term > -50.0) {
         double denom = sSquared * volTerm * bsModX[kX] * bsModY[kY] * bsModZ[kZ];
         expterm = exp(term) / denom;
         if (crystal.aperiodic()) {
           expterm *= (1.0 - cos(PI * crystal.a * sqrt(sSquared)));
         }
       }
       int ii = interleavedIndex(kX, kY, kZ, fftX, fftY) / 2;
       influenceFunction[ii] = expterm;
     }
 
     // Account for the zeroth grid point for a periodic system.
     influenceFunction[0] = 0.0;
     if (crystal.aperiodic()) {
       influenceFunction[0] = 0.5 * PI / crystal.a;
     }
 
     return influenceFunction;
   }
 
   private void transformMultipoleMatrix() {
     double[][] a = new double[3][3];
     for (int i = 0; i < 3; i++) {
       a[0][i] = fftX * crystal.A[i][0];
       a[1][i] = fftY * crystal.A[i][1];
       a[2][i] = fftZ * crystal.A[i][2];
     }
 
     for (int i = 0; i < 10; i++) {
       for (int j = 0; j < 10; j++) {
         transformMultipoleMatrix[i][j] = 0.0;
       }
     }
 
     // Charge
     transformMultipoleMatrix[0][0] = 1.0;
     // Dipole
     for (int i = 1; i < 4; i++) {
       arraycopy(a[i - 1], 0, transformMultipoleMatrix[i], 1, 3);
     }
     // Quadrupole
     for (int i1 = 0; i1 < 3; i1++) {
       int k = qi1[i1];
       for (int i2 = 0; i2 < 6; i2++) {
         int i = qi1[i2];
         int j = qi2[i2];
         transformMultipoleMatrix[i1 + 4][i2 + 4] = a[k][i] * a[k][j];
       }
     }
     for (int i1 = 3; i1 < 6; i1++) {
       int k = qi1[i1];
       int l = qi2[i1];
       for (int i2 = 0; i2 < 6; i2++) {
         int i = qi1[i2];
         int j = qi2[i2];
         transformMultipoleMatrix[i1 + 4][i2 + 4] = a[k][i] * a[l][j] + a[k][j] * a[l][i];
       }
     }
   }
 
   private void transformFieldMatrix() {
     double[][] a = new double[3][3];
 
     for (int i = 0; i < 3; i++) {
       a[i][0] = fftX * crystal.A[i][0];
       a[i][1] = fftY * crystal.A[i][1];
       a[i][2] = fftZ * crystal.A[i][2];
     }
     for (int i = 0; i < 10; i++) {
       for (int j = 0; j < 10; j++) {
         transformFieldMatrix[i][j] = 0.0;
       }
     }
     transformFieldMatrix[0][0] = 1.0;
     for (int i = 1; i < 4; i++) {
       arraycopy(a[i - 1], 0, transformFieldMatrix[i], 1, 3);
     }
     for (int i1 = 0; i1 < 3; i1++) {
       int k = qi1[i1];
       for (int i2 = 0; i2 < 3; i2++) {
         int i = qi1[i2];
         transformFieldMatrix[i1 + 4][i2 + 4] = a[k][i] * a[k][i];
       }
       for (int i2 = 3; i2 < 6; i2++) {
         int i = qi1[i2];
         int j = qi2[i2];
         transformFieldMatrix[i1 + 4][i2 + 4] = 2.0 * a[k][i] * a[k][j];
       }
     }
     for (int i1 = 3; i1 < 6; i1++) {
       int k = qi1[i1];
       int n = qi2[i1];
       for (int i2 = 0; i2 < 3; i2++) {
         int i = qi1[i2];
         transformFieldMatrix[i1 + 4][i2 + 4] = a[k][i] * a[n][i];
       }
       for (int i2 = 3; i2 < 6; i2++) {
         int i = qi1[i2];
         int j = qi2[i2];
         transformFieldMatrix[i1 + 4][i2 + 4] = a[k][i] * a[n][j] + a[n][i] * a[k][j];
       }
     }
   }
 
   /**
    * Convert a Cartesian multipole in the global frame into a factional multipole.
    *
    * @param gm Multipole in the global frame.
    * @param fm Fractional multipole.
    */
   private void toFractionalMultipole(double[] gm, double[] fm) {
     // Charge.
     fm[0] = gm[0];
 
     // Dipole.
     for (int j = 1; j < 4; j++) {
       fm[j] = 0.0;
       for (int k = 1; k < 4; k++) {
         fm[j] = fma(transformMultipoleMatrix[j][k], gm[k], fm[j]);
       }
     }
 
     // Quadrupole.
     for (int j = 4; j < 10; j++) {
       fm[j] = 0.0;
       for (int k = 4; k < 7; k++) {
         fm[j] = fma(transformMultipoleMatrix[j][k], gm[k], fm[j]);
       }
       for (int k = 7; k < 10; k++) {
         fm[j] = fma(transformMultipoleMatrix[j][k] * 2.0, gm[k], fm[j]);
       }
       /*
         Fractional quadrupole components are pre-multiplied by a
         factor of 1/3 that arises in their potential.
        */
       fm[j] = fm[j] * oneThird;
     }
   }
 
   /**
    * Convert a dipole in the global frame into a factional dipole.
    *
    * @param globalDipole     dipole in the global frame.
    * @param fractionalDipole fractional dipole.
    */
   public void toFractionalDipole(double[] globalDipole, double[] fractionalDipole) {
     for (int j = 0; j < 3; j++) {
       fractionalDipole[j] = 0.0;
       for (int k = 0; k < 3; k++) {
         fractionalDipole[j] = fma(transformMultipoleMatrix[j + 1][k + 1],
             globalDipole[k], fractionalDipole[j]);
       }
     }
   }
 
   public enum GridMethod {
     SPATIAL,
     SLICE,
     ROW
   }
 
   /**
    * The class computes b-Splines that are used to spline multipoles and induced dipoles onto the PME
    * grid. Following convolution, the b-Splines are then used to obtain the reciprocal space
    * potential and fields from the PME grid. This class automatically updates itself to be consistent
    * with the current Crystal boundary conditions.
    *
    * <p>An external ParallelRegion can be used as follows: <code>
    * start() { bSplineRegion.start(); } run() { execute(0, nAtoms - 1,
    * bSplineRegion.bSplineLoop[threadID]); }
    * </code>
    */
   public class BSplineRegion extends ParallelRegion {
 
     final BSplineLoop[] bSplineLoop;
     double[][][][] splineX;
     double[][][][] splineY;
     double[][][][] splineZ;
     int[][][] initGrid;
     private double r00;
     private double r01;
     private double r02;
     private double r10;
     private double r11;
     private double r12;
     private double r20;
     private double r21;
     private double r22;
 
     BSplineRegion() {
       bSplineLoop = new BSplineLoop[threadCount];
       for (int i = 0; i < threadCount; i++) {
         bSplineLoop[i] = new BSplineLoop();
       }
     }
 
     @Override
     public void run() {
       /*
        Currently this condition would indicate a programming bug, since
        the space group is not allowed to change and the ReciprocalSpace
        class should be operating on a unit cell with a fixed number of
        space group symmetry operators (and not a replicated unit cell).
       */
       if (splineX.length < nSymm) {
         logger.severe(
             " Programming Error: the number of reciprocal space symmetry operators changed.");
       }
       try {
         int threadID = getThreadIndex();
         execute(0, nAtoms - 1, bSplineLoop[threadID]);
       } catch (Exception e) {
         logger.severe(e.toString());
       }
     }
 
     @Override
     public void start() {
       r00 = crystal.A[0][0];
       r01 = crystal.A[0][1];
       r02 = crystal.A[0][2];
       r10 = crystal.A[1][0];
       r11 = crystal.A[1][1];
       r12 = crystal.A[1][2];
       r20 = crystal.A[2][0];
       r21 = crystal.A[2][1];
       r22 = crystal.A[2][2];
       if (splineX == null || splineX[0].length < nAtoms) {
         initGrid = new int[nSymm][nAtoms][];
         splineX = new double[nSymm][nAtoms][][];
         splineY = new double[nSymm][nAtoms][][];
         splineZ = new double[nSymm][nAtoms][][];
       }
     }
 
     public class BSplineLoop extends IntegerForLoop {
 
       private int threadID;
       private final double[][] bSplineWork;
       private final IntegerSchedule schedule = IntegerSchedule.fixed();
 
       BSplineLoop() {
         bSplineWork = new double[bSplineOrder][bSplineOrder];
       }
 
       @Override
       public void finish() {
         bSplineTime[threadID] += System.nanoTime();
       }
 
       @Override
       public void run(int lb, int ub) {
         for (int iSymOp = 0; iSymOp < nSymm; iSymOp++) {
           final double[] x = coordinates[iSymOp][0];
           final double[] y = coordinates[iSymOp][1];
           final double[] z = coordinates[iSymOp][2];
           final int[][] initgridi = initGrid[iSymOp];
           final double[][][] splineXi = splineX[iSymOp];
           final double[][][] splineYi = splineY[iSymOp];
           final double[][][] splineZi = splineZ[iSymOp];
           for (int i = lb; i <= ub; i++) {
             if (initgridi[i] == null) {
               initgridi[i] = new int[3];
               splineXi[i] = new double[bSplineOrder][derivOrder + 1];
               splineYi[i] = new double[bSplineOrder][derivOrder + 1];
               splineZi[i] = new double[bSplineOrder][derivOrder + 1];
             }
             final double xi = x[i];
             final double yi = y[i];
             final double zi = z[i];
             final int[] grd = initgridi[i];
             // X-dimension
             final double wx = xi * r00 + yi * r10 + zi * r20;
             final double ux = wx - round(wx) + 0.5;
             final double frx = fftX * ux;
             final int ifrx = (int) frx;
             final double bx = frx - ifrx;
             grd[0] = ifrx - bSplineOrder;
             bSplineDerivatives(bx, bSplineOrder, derivOrder, splineXi[i], bSplineWork);
             // Y-dimension
             final double wy = xi * r01 + yi * r11 + zi * r21;
             final double uy = wy - round(wy) + 0.5;
             final double fry = fftY * uy;
             final int ifry = (int) fry;
             final double by = fry - ifry;
             grd[1] = ifry - bSplineOrder;
             bSplineDerivatives(by, bSplineOrder, derivOrder, splineYi[i], bSplineWork);
             // Z-dimension
             final double wz = xi * r02 + yi * r12 + zi * r22;
             final double uz = wz - round(wz) + 0.5;
             final double frz = fftZ * uz;
             final int ifrz = (int) frz;
             final double bz = frz - ifrz;
             grd[2] = ifrz - bSplineOrder;
             bSplineDerivatives(bz, bSplineOrder, derivOrder, splineZi[i], bSplineWork);
           }
         }
       }
 
       @Override
       public IntegerSchedule schedule() {
         return schedule;
       }
 
       @Override
       public void start() {
         threadID = getThreadIndex();
         bSplineTime[threadID] -= System.nanoTime();
       }
     }
   }
 
   private class SpatialPermanentLoop extends SpatialDensityLoop {
 
     private final BSplineRegion bSplines;
     private double[][][] fracMultipoles = null;
     private boolean[] use = null;
     private int threadIndex;
 
     SpatialPermanentLoop(SpatialDensityRegion region, BSplineRegion splines) {
       super(region, region.nSymm, region.actualCount);
       this.bSplines = splines;
     }
 
     @Override
     public void finish() {
       splinePermanentTime[threadIndex] += System.nanoTime();
     }
 
     @Override
     public void gridDensity(int iSymm, int n) {
       // Some atoms are not used during Lambda dynamics.
       if (use != null && !use[n]) {
         return;
       }
       splineCount[threadIndex]++;
       switch (elecForm) {
         case PAM -> gridMultipoleDensity(iSymm, n);
         case FIXED_CHARGE -> gridFixedChargeDensity(iSymm, n);
       }
     }
 
     private void gridMultipoleDensity(int iSymm, int n) {
       final double[] fm = fracMultipoles[iSymm][n];
       final double[][] splx = bSplines.splineX[iSymm][n];
       final double[][] sply = bSplines.splineY[iSymm][n];
       final double[][] splz = bSplines.splineZ[iSymm][n];
       final int igrd0 = bSplines.initGrid[iSymm][n][0];
       final int jgrd0 = bSplines.initGrid[iSymm][n][1];
       int k0 = bSplines.initGrid[iSymm][n][2];
       final double c = fm[t000];
       final double dx = fm[t100];
       final double dy = fm[t010];
       final double dz = fm[t001];
       final double qxx = fm[t200];
       final double qyy = fm[t020];
       final double qzz = fm[t002];
       final double qxy = fm[t110];
       final double qxz = fm[t101];
       final double qyz = fm[t011];
       for (int ith3 = 0; ith3 < bSplineOrder; ith3++) {
         final double[] splzi = splz[ith3];
         final double v0 = splzi[0];
         final double v1 = splzi[1];
         final double v2 = splzi[2];
         final double c0 = c * v0;
         final double dx0 = dx * v0;
         final double dy0 = dy * v0;
         final double dz1 = dz * v1;
         final double qxx0 = qxx * v0;
         final double qyy0 = qyy * v0;
         final double qzz2 = qzz * v2;
         final double qxy0 = qxy * v0;
         final double qxz1 = qxz * v1;
         final double qyz1 = qyz * v1;
         final double c0dz1qzz2 = c0 + dz1 + qzz2;
         final double dy0qyz1 = dy0 + qyz1;
         final double dx0qxz1 = dx0 + qxz1;
         final int k = mod(++k0, fftZ);
         int j0 = jgrd0;
         for (int ith2 = 0; ith2 < bSplineOrder; ith2++) {
           final double[] splyi = sply[ith2];
           final double u0 = splyi[0];
           final double u1 = splyi[1];
           final double u2 = splyi[2];
           final double term0 = fma(c0dz1qzz2, u0, fma(dy0qyz1, u1, qyy0 * u2));
           final double term1 = fma(dx0qxz1, u0, qxy0 * u1);
           final double term2 = qxx0 * u0;
           final int j = mod(++j0, fftY);
           int i0 = igrd0;
           for (int ith1 = 0; ith1 < bSplineOrder; ith1++) {
             final int i = mod(++i0, fftX);
             final int ii = interleavedIndex(i, j, k, fftX, fftY);
             final double[] splxi = splx[ith1];
             final double current = splineBuffer.get(ii);
             double updated = fma(splxi[0], term0, current);
             updated = fma(splxi[1], term1, updated);
             updated = fma(splxi[2], term2, updated);
             splineBuffer.put(ii, updated);
           }
         }
       }
     }
 
     private void gridFixedChargeDensity(int iSymm, int n) {
       final double[] fm = fracMultipoles[iSymm][n];
       final double[][] splx = bSplines.splineX[iSymm][n];
       final double[][] sply = bSplines.splineY[iSymm][n];
       final double[][] splz = bSplines.splineZ[iSymm][n];
       final int igrd0 = bSplines.initGrid[iSymm][n][0];
       final int jgrd0 = bSplines.initGrid[iSymm][n][1];
       int k0 = bSplines.initGrid[iSymm][n][2];
       final double c = fm[t000];
       for (int ith3 = 0; ith3 < bSplineOrder; ith3++) {
         final double[] splzi = splz[ith3];
         final double v0 = splzi[0];
         final double c0 = c * v0;
         final int k = mod(++k0, fftZ);
         int j0 = jgrd0;
         for (int ith2 = 0; ith2 < bSplineOrder; ith2++) {
           final double[] splyi = sply[ith2];
           final double u0 = splyi[0];
           final double term0 = c0 * u0;
           final int j = mod(++j0, fftY);
           int i0 = igrd0;
           for (int ith1 = 0; ith1 < bSplineOrder; ith1++) {
             final int i = mod(++i0, fftX);
             final int ii = interleavedIndex(i, j, k, fftX, fftY);
             final double[] splxi = splx[ith1];
             final double current = splineBuffer.get(ii);
             double updated = fma(splxi[0], term0, current);
             splineBuffer.put(ii, updated);
           }
         }
       }
     }
 
     @Override
     public void start() {
       threadIndex = getThreadIndex();
       splinePermanentTime[threadIndex] -= System.nanoTime();
     }
 
     void setPermanent(double[][][] fracMultipoles) {
       this.fracMultipoles = fracMultipoles;
     }
 
     private void setUse(boolean[] use) {
       this.use = use;
     }
   }
 
   private class SpatialInducedLoop extends SpatialDensityLoop {
 
     private final BSplineRegion bSplineRegion;
     private double[][][] inducedDipoleFrac = null;
     private double[][][] inducedDipoleFracCR = null;
     private boolean[] use = null;
 
     SpatialInducedLoop(SpatialDensityRegion region, BSplineRegion splines) {
       super(region, region.nSymm, region.actualCount);
       this.bSplineRegion = splines;
     }
 
     @Override
     public void finish() {
       splineInducedTime[getThreadIndex()] += System.nanoTime();
     }
 
     @Override
     public void gridDensity(int iSymm, int n) {
       if (use != null && !use[n]) {
         return;
       }
 
       // Convert Cartesian induced dipole to fractional induced dipole.
       final double[] ind = inducedDipoleFrac[iSymm][n];
       final double ux = ind[0];
       final double uy = ind[1];
       final double uz = ind[2];
       final double[] indCR = inducedDipoleFracCR[iSymm][n];
       final double px = indCR[0];
       final double py = indCR[1];
       final double pz = indCR[2];
       final double[][] splx = bSplineRegion.splineX[iSymm][n];
       final double[][] sply = bSplineRegion.splineY[iSymm][n];
       final double[][] splz = bSplineRegion.splineZ[iSymm][n];
       final int igrd0 = bSplineRegion.initGrid[iSymm][n][0];
       final int jgrd0 = bSplineRegion.initGrid[iSymm][n][1];
       int k0 = bSplineRegion.initGrid[iSymm][n][2];
       for (int ith3 = 0; ith3 < bSplineOrder; ith3++) {
         final double[] splzi = splz[ith3];
         final double v0 = splzi[0];
         final double v1 = splzi[1];
         final double dx0 = ux * v0;
         final double dy0 = uy * v0;
         final double dz1 = uz * v1;
         final double px0 = px * v0;
         final double py0 = py * v0;
         final double pz1 = pz * v1;
         final int k = mod(++k0, fftZ);
         int j0 = jgrd0;
         for (int ith2 = 0; ith2 < bSplineOrder; ith2++) {
           final double[] splyi = sply[ith2];
           final double u0 = splyi[0];
           final double u1 = splyi[1];
           final double term0 = fma(dz1, u0, dy0 * u1);
           final double term1 = dx0 * u0;
           final double termp0 = fma(pz1, u0, py0 * u1);
           final double termp1 = px0 * u0;
           final int j = mod(++j0, fftY);
           int i0 = igrd0;
           for (int ith1 = 0; ith1 < bSplineOrder; ith1++) {
             final int i = mod(++i0, fftX);
             final int ii = interleavedIndex(i, j, k, fftX, fftY);
             final double[] splxi = splx[ith1];
             final double current = splineBuffer.get(ii);
             final double currenti = splineBuffer.get(ii + 1);
             final double updated = fma(splxi[0], term0, fma(splxi[1], term1, current));
             final double udpatedi = fma(splxi[0], termp0, fma(splxi[1], termp1, currenti));
             splineBuffer.put(ii, updated);
             splineBuffer.put(ii + 1, udpatedi);
           }
         }
       }
     }
 
     public void setUse(boolean[] use) {
       this.use = use;
     }
 
     @Override
     public void start() {
       splineInducedTime[getThreadIndex()] -= System.nanoTime();
     }
 
     void setInducedDipoles(double[][][] inducedDipoleFrac, double[][][] inducedDipoleFracCR) {
       this.inducedDipoleFrac = inducedDipoleFrac;
       this.inducedDipoleFracCR = inducedDipoleFracCR;
     }
   }
 
   private class RowPermanentLoop extends RowLoop {
 
     private final BSplineRegion bSplines;
     private double[][][] fracMultipoles = null;
     private boolean[] use = null;
     private int threadIndex;
 
     RowPermanentLoop(RowRegion region, BSplineRegion splines) {
       super(region.nAtoms, region.nSymm, region);
       this.bSplines = splines;
     }
 
     @Override
     public void finish() {
       splinePermanentTime[threadIndex] += System.nanoTime();
     }
 
     @Override
     public void gridDensity(int iSymm, int iAtom, int lb, int ub) {
       // Some atoms are not used during Lambda dynamics.
       if (use != null && !use[iAtom]) {
         return;
       }
       switch (elecForm) {
         case PAM -> gridMultipoleDensity(iSymm, iAtom, lb, ub);
         case FIXED_CHARGE -> gridFixedChargeDensity(iSymm, iAtom, lb, ub);
       }
     }
 
     private void gridMultipoleDensity(int iSymm, int iAtom, int lb, int ub) {
       boolean atomContributes = false;
       int k0 = bSplines.initGrid[iSymm][iAtom][2];
       int lbZ = RowIndexZ(lb);
       int ubZ = RowIndexZ(ub);
       for (int ith3 = 0; ith3 < bSplineOrder; ith3++) {
         final int k = mod(++k0, fftZ);
         if (lbZ <= k && k <= ubZ) {
           atomContributes = true;
           break;
         }
       }
       if (!atomContributes) {
         return;
       }
 
       splineCount[threadIndex]++;
 
       // Add atom n to the list for the current symmOp and thread.
       int index = gridAtomCount[iSymm][threadIndex];
       gridAtomList[iSymm][threadIndex][index] = iAtom;
       gridAtomCount[iSymm][threadIndex]++;
       final double[] fm = fracMultipoles[iSymm][iAtom];
       final double[][] splx = bSplines.splineX[iSymm][iAtom];
       final double[][] sply = bSplines.splineY[iSymm][iAtom];
       final double[][] splz = bSplines.splineZ[iSymm][iAtom];
       final int igrd0 = bSplines.initGrid[iSymm][iAtom][0];
       final int jgrd0 = bSplines.initGrid[iSymm][iAtom][1];
       k0 = bSplines.initGrid[iSymm][iAtom][2];
       final double c = fm[t000];
       final double dx = fm[t100];
       final double dy = fm[t010];
       final double dz = fm[t001];
       final double qxx = fm[t200];
       final double qyy = fm[t020];
       final double qzz = fm[t002];
       final double qxy = fm[t110];
       final double qxz = fm[t101];
       final double qyz = fm[t011];
       for (int ith3 = 0; ith3 < bSplineOrder; ith3++) {
         final int k = mod(++k0, fftZ);
         if (k < lbZ || k > ubZ) {
           continue;
         }
         final double[] splzi = splz[ith3];
         final double v0 = splzi[0];
         final double v1 = splzi[1];
         final double v2 = splzi[2];
         final double c0 = c * v0;
         final double dx0 = dx * v0;
         final double dy0 = dy * v0;
         final double dz1 = dz * v1;
         final double qxx0 = qxx * v0;
         final double qyy0 = qyy * v0;
         final double qzz2 = qzz * v2;
         final double qxy0 = qxy * v0;
         final double qxz1 = qxz * v1;
         final double qyz1 = qyz * v1;
         final double c0dz1qzz2 = c0 + dz1 + qzz2;
         final double dy0qyz1 = dy0 + qyz1;
         final double dx0qxz1 = dx0 + qxz1;
         int j0 = jgrd0;
         for (int ith2 = 0; ith2 < bSplineOrder; ith2++) {
           final int j = mod(++j0, fftY);
           int rowIndex = rowRegion.rowIndexForYZ(j, k);
           if (lb > rowIndex || rowIndex > ub) {
             continue;
           }
           final double[] splyi = sply[ith2];
           final double u0 = splyi[0];
           final double u1 = splyi[1];
           final double u2 = splyi[2];
           // Pieces of a multipole
           final double term0 = fma(c0dz1qzz2, u0, fma(dy0qyz1, u1, qyy0 * u2));
           final double term1 = fma(dx0qxz1, u0, qxy0 * u1);
           final double term2 = qxx0 * u0;
           int i0 = igrd0;
           for (int ith1 = 0; ith1 < bSplineOrder; ith1++) {
             final int i = mod(++i0, fftX);
             final int ii = interleavedIndex(i, j, k, fftX, fftY);
             final double[] splxi = splx[ith1];
             double current = splineBuffer.get(ii);
             double updated = fma(splxi[0], term0, current);
             updated = fma(splxi[1], term1, updated);
             updated = fma(splxi[2], term2, updated);
             splineBuffer.put(ii, updated);
           }
         }
       }
     }
 
     private void gridFixedChargeDensity(int iSymm, int iAtom, int lb, int ub) {
       boolean atomContributes = false;
       int k0 = bSplines.initGrid[iSymm][iAtom][2];
       int lbZ = RowIndexZ(lb);
       int ubZ = RowIndexZ(ub);
       for (int ith3 = 0; ith3 < bSplineOrder; ith3++) {
         final int k = mod(++k0, fftZ);
         if (lbZ <= k && k <= ubZ) {
           atomContributes = true;
           break;
         }
       }
       if (!atomContributes) {
         return;
       }
 
       splineCount[threadIndex]++;
 
       // Add atom n to the list for the current symmOp and thread.
       int index = gridAtomCount[iSymm][threadIndex];
       gridAtomList[iSymm][threadIndex][index] = iAtom;
       gridAtomCount[iSymm][threadIndex]++;
       final double[] fm = fracMultipoles[iSymm][iAtom];
       final double[][] splx = bSplines.splineX[iSymm][iAtom];
       final double[][] sply = bSplines.splineY[iSymm][iAtom];
       final double[][] splz = bSplines.splineZ[iSymm][iAtom];
       final int igrd0 = bSplines.initGrid[iSymm][iAtom][0];
       final int jgrd0 = bSplines.initGrid[iSymm][iAtom][1];
       k0 = bSplines.initGrid[iSymm][iAtom][2];
       final double c = fm[t000];
       for (int ith3 = 0; ith3 < bSplineOrder; ith3++) {
         final int k = mod(++k0, fftZ);
         if (k < lbZ || k > ubZ) {
           continue;
         }
         final double[] splzi = splz[ith3];
         final double v0 = splzi[0];
         final double c0 = c * v0;
         int j0 = jgrd0;
         for (int ith2 = 0; ith2 < bSplineOrder; ith2++) {
           final int j = mod(++j0, fftY);
           int rowIndex = rowRegion.rowIndexForYZ(j, k);
           if (lb > rowIndex || rowIndex > ub) {
             continue;
           }
           final double[] splyi = sply[ith2];
           final double u0 = splyi[0];
           // Pieces of a multipole
           final double term0 = c0 * u0;
           int i0 = igrd0;
           for (int ith1 = 0; ith1 < bSplineOrder; ith1++) {
             final int i = mod(++i0, fftX);
             final int ii = interleavedIndex(i, j, k, fftX, fftY);
             final double[] splxi = splx[ith1];
             double current = splineBuffer.get(ii);
             double updated = fma(splxi[0], term0, current);
             splineBuffer.put(ii, updated);
           }
         }
       }
     }
 
     @Override
     public void start() {
       threadIndex = getThreadIndex();
       splinePermanentTime[threadIndex] -= System.nanoTime();
       for (int i = 0; i < nSymm; i++) {
         gridAtomCount[i][threadIndex] = 0;
       }
     }
 
     void setPermanent(double[][][] fracMultipoles) {
       this.fracMultipoles = fracMultipoles;
     }
 
     private void setUse(boolean[] use) {
       this.use = use;
     }
   }
 
   private class RowInducedLoop extends RowLoop {
 
     private final BSplineRegion bSplineRegion;
     private double[][][] inducedDipoleFrac = null;
     private double[][][] inducedDipoleFracCR = null;
     private boolean[] use = null;
 
     RowInducedLoop(RowRegion region, BSplineRegion splines) {
       super(region.nAtoms, region.nSymm, region);
       this.bSplineRegion = splines;
     }
 
     @Override
     public void finish() {
       int threadIndex = getThreadIndex();
       splineInducedTime[threadIndex] += System.nanoTime();
     }
 
     @Override
     public void gridDensity(int iSymm, int iAtom, int lb, int ub) {
       if (use != null && !use[iAtom]) {
         return;
       }
 
       final int lbZ = RowIndexZ(lb);
       final int ubZ = RowIndexZ(ub);
       final double[] ind = inducedDipoleFrac[iSymm][iAtom];
       final double ux = ind[0];
       final double uy = ind[1];
       final double uz = ind[2];
       double[] indCR = inducedDipoleFracCR[iSymm][iAtom];
       final double px = indCR[0];
       final double py = indCR[1];
       final double pz = indCR[2];
       final double[][] splx = bSplineRegion.splineX[iSymm][iAtom];
       final double[][] sply = bSplineRegion.splineY[iSymm][iAtom];
       final double[][] splz = bSplineRegion.splineZ[iSymm][iAtom];
       final int igrd0 = bSplineRegion.initGrid[iSymm][iAtom][0];
       final int jgrd0 = bSplineRegion.initGrid[iSymm][iAtom][1];
       int k0 = bSplineRegion.initGrid[iSymm][iAtom][2];
       for (int ith3 = 0; ith3 < bSplineOrder; ith3++) {
         final int k = mod(++k0, fftZ);
         if (k < lbZ || k > ubZ) {
           continue;
         }
         final double[] splzi = splz[ith3];
         final double v0 = splzi[0];
         final double v1 = splzi[1];
         final double dx0 = ux * v0;
         final double dy0 = uy * v0;
         final double dz1 = uz * v1;
         final double px0 = px * v0;
         final double py0 = py * v0;
         final double pz1 = pz * v1;
         int j0 = jgrd0;
         for (int ith2 = 0; ith2 < bSplineOrder; ith2++) {
           final int j = mod(++j0, fftY);
           int rowIndex = rowRegion.rowIndexForYZ(j, k);
           if (lb > rowIndex || rowIndex > ub) {
             continue;
           }
           final double[] splyi = sply[ith2];
           final double u0 = splyi[0];
           final double u1 = splyi[1];
           final double term0 = fma(dz1, u0, dy0 * u1);
           final double term1 = dx0 * u0;
           final double termp0 = fma(pz1, u0, py0 * u1);
           final double termp1 = px0 * u0;
           int i0 = igrd0;
           for (int ith1 = 0; ith1 < bSplineOrder; ith1++) {
             final int i = mod(++i0, fftX);
             final int ii = interleavedIndex(i, j, k, fftX, fftY);
             final double[] splxi = splx[ith1];
             final double current = splineBuffer.get(ii);
             final double currenti = splineBuffer.get(ii + 1);
             final double updated = fma(splxi[0], term0, fma(splxi[1], term1, current));
             final double udpatedi = fma(splxi[0], termp0, fma(splxi[1], termp1, currenti));
             splineBuffer.put(ii, updated);
             splineBuffer.put(ii + 1, udpatedi);
           }
         }
       }
     }
 
     @Override
     public void run(int lb, int ub) {
       int ti = getThreadIndex();
       for (int iSymm = 0; iSymm < nSymm; iSymm++) {
         int[] list = gridAtomList[iSymm][ti];
         int n = gridAtomCount[iSymm][ti];
         for (int i = 0; i < n; i++) {
           int iAtom = list[i];
           gridDensity(iSymm, iAtom, lb, ub);
         }
       }
     }
 
     public void setUse(boolean[] use) {
       this.use = use;
     }
 
     @Override
     public void start() {
       int threadIndex = getThreadIndex();
       splineInducedTime[threadIndex] -= System.nanoTime();
     }
 
     void setInducedDipoles(double[][][] inducedDipoleFrac, double[][][] inducedDipoleFracCR) {
       this.inducedDipoleFrac = inducedDipoleFrac;
       this.inducedDipoleFracCR = inducedDipoleFracCR;
     }
   }
 
   private class SlicePermanentLoop extends SliceLoop {
 
     private final BSplineRegion bSplines;
     private double[][][] fracMultipoles = null;
     private boolean[] use = null;
     private int threadIndex;
 
     SlicePermanentLoop(SliceRegion region, BSplineRegion splines) {
       super(region.nAtoms, region.nSymm, region);
       this.bSplines = splines;
     }
 
     @Override
     public void finish() {
       splinePermanentTime[threadIndex] += System.nanoTime();
     }
 
     @Override
     public void gridDensity(int iSymm, int iAtom, int lb, int ub) {
       // Some atoms are not used during Lambda dynamics.
       if (use != null && !use[iAtom]) {
         return;
       }
 
       switch (elecForm) {
         case PAM -> gridMultipoleDensity(iSymm, iAtom, lb, ub);
         case FIXED_CHARGE -> gridFixedChargeDensity(iSymm, iAtom, lb, ub);
       }
     }
 
     private void gridMultipoleDensity(int iSymm, int iAtom, int lb, int ub) {
       boolean atomContributes = false;
       int k0 = bSplines.initGrid[iSymm][iAtom][2];
       for (int ith3 = 0; ith3 < bSplineOrder; ith3++) {
         final int k = mod(++k0, fftZ);
         if (lb <= k && k <= ub) {
           atomContributes = true;
           break;
         }
       }
       if (!atomContributes) {
         return;
       }
 
       splineCount[threadIndex]++;
 
       // Add atom n to the list for the current symmOp and thread.
       int index = gridAtomCount[iSymm][threadIndex];
       gridAtomList[iSymm][threadIndex][index] = iAtom;
       gridAtomCount[iSymm][threadIndex]++;
       final double[] fm = fracMultipoles[iSymm][iAtom];
       final double[][] splx = bSplines.splineX[iSymm][iAtom];
       final double[][] sply = bSplines.splineY[iSymm][iAtom];
       final double[][] splz = bSplines.splineZ[iSymm][iAtom];
       final int igrd0 = bSplines.initGrid[iSymm][iAtom][0];
       final int jgrd0 = bSplines.initGrid[iSymm][iAtom][1];
       k0 = bSplines.initGrid[iSymm][iAtom][2];
       final double c = fm[t000];
       final double dx = fm[t100];
       final double dy = fm[t010];
       final double dz = fm[t001];
       final double qxx = fm[t200];
       final double qyy = fm[t020];
       final double qzz = fm[t002];
       final double qxy = fm[t110];
       final double qxz = fm[t101];
       final double qyz = fm[t011];
       for (int ith3 = 0; ith3 < bSplineOrder; ith3++) {
         final int k = mod(++k0, fftZ);
         if (k < lb || k > ub) {
           continue;
         }
         final double[] splzi = splz[ith3];
         final double v0 = splzi[0];
         final double v1 = splzi[1];
         final double v2 = splzi[2];
         final double c0 = c * v0;
         final double dx0 = dx * v0;
         final double dy0 = dy * v0;
         final double dz1 = dz * v1;
         final double qxx0 = qxx * v0;
         final double qyy0 = qyy * v0;
         final double qzz2 = qzz * v2;
         final double qxy0 = qxy * v0;
         final double qxz1 = qxz * v1;
         final double qyz1 = qyz * v1;
         final double c0dz1qzz2 = c0 + dz1 + qzz2;
         final double dy0qyz1 = dy0 + qyz1;
         final double dx0qxz1 = dx0 + qxz1;
         int j0 = jgrd0;
         for (int ith2 = 0; ith2 < bSplineOrder; ith2++) {
           final double[] splyi = sply[ith2];
           final double u0 = splyi[0];
           final double u1 = splyi[1];
           final double u2 = splyi[2];
           // Pieces of a multipole
           final double term0 = fma(c0dz1qzz2, u0, fma(dy0qyz1, u1, qyy0 * u2));
           final double term1 = fma(dx0qxz1, u0, qxy0 * u1);
           final double term2 = qxx0 * u0;
           final int j = mod(++j0, fftY);
           int i0 = igrd0;
           for (int ith1 = 0; ith1 < bSplineOrder; ith1++) {
             final int i = mod(++i0, fftX);
             final int ii = interleavedIndex(i, j, k, fftX, fftY);
             final double[] splxi = splx[ith1];
             double current = splineBuffer.get(ii);
             double updated = fma(splxi[0], term0, current);
             updated = fma(splxi[1], term1, updated);
             updated = fma(splxi[2], term2, updated);
             splineBuffer.put(ii, updated);
           }
         }
       }
     }
 
     private void gridFixedChargeDensity(int iSymm, int iAtom, int lb, int ub) {
       boolean atomContributes = false;
       int k0 = bSplines.initGrid[iSymm][iAtom][2];
       for (int ith3 = 0; ith3 < bSplineOrder; ith3++) {
         final int k = mod(++k0, fftZ);
         if (lb <= k && k <= ub) {
           atomContributes = true;
           break;
         }
       }
       if (!atomContributes) {
         return;
       }
 
       splineCount[threadIndex]++;
 
       // Add atom n to the list for the current symmOp and thread.
       int index = gridAtomCount[iSymm][threadIndex];
       gridAtomList[iSymm][threadIndex][index] = iAtom;
       gridAtomCount[iSymm][threadIndex]++;
       final double[] fm = fracMultipoles[iSymm][iAtom];
       final double[][] splx = bSplines.splineX[iSymm][iAtom];
       final double[][] sply = bSplines.splineY[iSymm][iAtom];
       final double[][] splz = bSplines.splineZ[iSymm][iAtom];
       final int igrd0 = bSplines.initGrid[iSymm][iAtom][0];
       final int jgrd0 = bSplines.initGrid[iSymm][iAtom][1];
       k0 = bSplines.initGrid[iSymm][iAtom][2];
       final double c = fm[t000];
       for (int ith3 = 0; ith3 < bSplineOrder; ith3++) {
         final int k = mod(++k0, fftZ);
         if (k < lb || k > ub) {
           continue;
         }
         final double[] splzi = splz[ith3];
         final double v0 = splzi[0];
         final double c0 = c * v0;
         int j0 = jgrd0;
         for (int ith2 = 0; ith2 < bSplineOrder; ith2++) {
           final double[] splyi = sply[ith2];
           final double u0 = splyi[0];
           final double term0 = c0 * u0;
           final int j = mod(++j0, fftY);
           int i0 = igrd0;
           for (int ith1 = 0; ith1 < bSplineOrder; ith1++) {
             final int i = mod(++i0, fftX);
             final int ii = interleavedIndex(i, j, k, fftX, fftY);
             final double[] splxi = splx[ith1];
             double current = splineBuffer.get(ii);
             double updated = fma(splxi[0], term0, current);
             splineBuffer.put(ii, updated);
           }
         }
       }
     }
 
     @Override
     public void start() {
       threadIndex = getThreadIndex();
       splinePermanentTime[threadIndex] -= System.nanoTime();
       for (int i = 0; i < nSymm; i++) {
         gridAtomCount[i][threadIndex] = 0;
       }
     }
 
     void setPermanent(double[][][] fracMultipoles) {
       this.fracMultipoles = fracMultipoles;
     }
 
     private void setUse(boolean[] use) {
       this.use = use;
     }
   }
 
   private class SliceInducedLoop extends SliceLoop {
 
     private final BSplineRegion bSplineRegion;
     private double[][][] inducedDipoleFrac = null;
     private double[][][] inducedDipoleFracCR = null;
     private boolean[] use = null;
 
     SliceInducedLoop(SliceRegion region, BSplineRegion splines) {
       super(region.nAtoms, region.nSymm, region);
       this.bSplineRegion = splines;
     }
 
     @Override
     public void finish() {
       int threadIndex = getThreadIndex();
       splineInducedTime[threadIndex] += System.nanoTime();
     }
 
     @Override
     public void gridDensity(int iSymm, int iAtom, int lb, int ub) {
       if (use != null && !use[iAtom]) {
         return;
       }
 
       // Convert Cartesian induced dipole to fractional induced dipole.
       double[] ind = inducedDipoleFrac[iSymm][iAtom];
       double ux = ind[0];
       double uy = ind[1];
       double uz = ind[2];
       double[] indCR = inducedDipoleFracCR[iSymm][iAtom];
       double px = indCR[0];
       double py = indCR[1];
       double pz = indCR[2];
       final double[][] splx = bSplineRegion.splineX[iSymm][iAtom];
       final double[][] sply = bSplineRegion.splineY[iSymm][iAtom];
       final double[][] splz = bSplineRegion.splineZ[iSymm][iAtom];
       final int igrd0 = bSplineRegion.initGrid[iSymm][iAtom][0];
       final int jgrd0 = bSplineRegion.initGrid[iSymm][iAtom][1];
       int k0 = bSplineRegion.initGrid[iSymm][iAtom][2];
       for (int ith3 = 0; ith3 < bSplineOrder; ith3++) {
         final int k = mod(++k0, fftZ);
         if (k < lb || k > ub) {
           continue;
         }
         final double[] splzi = splz[ith3];
         final double v0 = splzi[0];
         final double v1 = splzi[1];
         final double dx0 = ux * v0;
         final double dy0 = uy * v0;
         final double dz1 = uz * v1;
         final double px0 = px * v0;
         final double py0 = py * v0;
         final double pz1 = pz * v1;
         int j0 = jgrd0;
         for (int ith2 = 0; ith2 < bSplineOrder; ith2++) {
           final double[] splyi = sply[ith2];
           final double u0 = splyi[0];
           final double u1 = splyi[1];
           final double term0 = fma(dz1, u0, dy0 * u1);
           final double term1 = dx0 * u0;
           final double termp0 = fma(pz1, u0, py0 * u1);
           final double termp1 = px0 * u0;
           final int j = mod(++j0, fftY);
           int i0 = igrd0;
           for (int ith1 = 0; ith1 < bSplineOrder; ith1++) {
             final int i = mod(++i0, fftX);
             final int ii = interleavedIndex(i, j, k, fftX, fftY);
             final double[] splxi = splx[ith1];
             final double current = splineBuffer.get(ii);
             final double currenti = splineBuffer.get(ii + 1);
             final double updated = fma(splxi[0], term0, fma(splxi[1], term1, current));
             final double udpatedi = fma(splxi[0], termp0, fma(splxi[1], termp1, currenti));
             splineBuffer.put(ii, updated);
             splineBuffer.put(ii + 1, udpatedi);
           }
         }
       }
     }
 
     @Override
     public void run(int lb, int ub) {
       int ti = getThreadIndex();
       for (int iSymm = 0; iSymm < nSymm; iSymm++) {
         int[] list = gridAtomList[iSymm][ti];
         int n = gridAtomCount[iSymm][ti];
         for (int i = 0; i < n; i++) {
           int iAtom = list[i];
           gridDensity(iSymm, iAtom, lb, ub);
         }
       }
     }
 
     public void setUse(boolean[] use) {
       this.use = use;
     }
 
     @Override
     public void start() {
       int threadIndex = getThreadIndex();
       splineInducedTime[threadIndex] -= System.nanoTime();
     }
 
     void setInducedDipoles(double[][][] inducedDipoleFrac, double[][][] inducedDipoleFracCR) {
       this.inducedDipoleFrac = inducedDipoleFrac;
       this.inducedDipoleFracCR = inducedDipoleFracCR;
     }
   }
 
   /**
    * This class is used to obtain the reciprocal space potential and fields due to permanent
    * multipoles from the PME grid.
    *
    * <p>An external ParallelRegion can be used as follows: <code>
    * start() { permanentPhiRegion.setCartPermanentPhi(...); }
    * <p>
    * run() { execute(0, nAtoms - 1, permanentPhiLoops[threadID]); }
    * </code>
    */
   private class PermanentPhiRegion extends ParallelRegion {
 
     final PermanentPhiLoop[] permanentPhiLoop;
 
     private final BSplineRegion bSplineRegion;
     private double[][] cartPermPhi;
     private double[][] fracPermPhi;
 
     PermanentPhiRegion(BSplineRegion bSplineRegion) {
       this.bSplineRegion = bSplineRegion;
       permanentPhiLoop = new PermanentPhiLoop[threadCount];
       for (int i = 0; i < threadCount; i++) {
         permanentPhiLoop[i] = new PermanentPhiLoop();
       }
     }
 
     @Override
     public void run() {
       try {
         int threadID = getThreadIndex();
         execute(0, nAtoms - 1, permanentPhiLoop[threadID]);
       } catch (Exception e) {
         logger.severe(e.toString());
       }
     }
 
     void setPermanentPhi(double[][] cartPermanentPhi, double[][] fracPermanentPhi) {
       this.cartPermPhi = cartPermanentPhi;
       this.fracPermPhi = fracPermanentPhi;
     }
 
     public class PermanentPhiLoop extends IntegerForLoop {
 
       @Override
       public void finish() {
         int threadIndex = getThreadIndex();
         permanentPhiTime[threadIndex] += System.nanoTime();
       }
 
       @Override
       public void run(final int lb, final int ub) {
         for (int n = lb; n <= ub; n++) {
           final double[][] splx = bSplineRegion.splineX[0][n];
           final double[][] sply = bSplineRegion.splineY[0][n];
           final double[][] splz = bSplineRegion.splineZ[0][n];
           final int[] igrd = bSplineRegion.initGrid[0][n];
           final int igrd0 = igrd[0];
           final int jgrd0 = igrd[1];
           int k0 = igrd[2];
           double tuv000 = 0.0;
           double tuv100 = 0.0;
           double tuv010 = 0.0;
           double tuv001 = 0.0;
           double tuv200 = 0.0;
           double tuv020 = 0.0;
           double tuv002 = 0.0;
           double tuv110 = 0.0;
           double tuv101 = 0.0;
           double tuv011 = 0.0;
           double tuv300 = 0.0;
           double tuv030 = 0.0;
           double tuv003 = 0.0;
           double tuv210 = 0.0;
           double tuv201 = 0.0;
           double tuv120 = 0.0;
           double tuv021 = 0.0;
           double tuv102 = 0.0;
           double tuv012 = 0.0;
           double tuv111 = 0.0;
           for (int ith3 = 0; ith3 < bSplineOrder; ith3++) {
             final int k = mod(++k0, fftZ);
             int j0 = jgrd0;
             double tu00 = 0.0;
             double tu10 = 0.0;
             double tu01 = 0.0;
             double tu20 = 0.0;
             double tu11 = 0.0;
             double tu02 = 0.0;
             double tu30 = 0.0;
             double tu21 = 0.0;
             double tu12 = 0.0;
             double tu03 = 0.0;
             for (int ith2 = 0; ith2 < bSplineOrder; ith2++) {
               final int j = mod(++j0, fftY);
               int i0 = igrd0;
               double t0 = 0.0;
               double t1 = 0.0;
               double t2 = 0.0;
               double t3 = 0.0;
               for (int ith1 = 0; ith1 < bSplineOrder; ith1++) {
                 final int i = mod(++i0, fftX);
                 final int ii = interleavedIndex(i, j, k, fftX, fftY);
                 final double tq = splineBuffer.get(ii);
                 final double[] splxi = splx[ith1];
                 t0 = fma(tq, splxi[0], t0);
                 t1 = fma(tq, splxi[1], t1);
                 t2 = fma(tq, splxi[2], t2);
                 t3 = fma(tq, splxi[3], t3);
               }
               final double[] splyi = sply[ith2];
               final double u0 = splyi[0];
               final double u1 = splyi[1];
               final double u2 = splyi[2];
               final double u3 = splyi[3];
               tu00 = fma(t0, u0, tu00);
               tu10 = fma(t1, u0, tu10);
               tu01 = fma(t0, u1, tu01);
               tu20 = fma(t2, u0, tu20);
               tu11 = fma(t1, u1, tu11);
               tu02 = fma(t0, u2, tu02);
               tu30 = fma(t3, u0, tu30);
               tu21 = fma(t2, u1, tu21);
               tu12 = fma(t1, u2, tu12);
               tu03 = fma(t0, u3, tu03);
             }
             final double[] splzi = splz[ith3];
             final double v0 = splzi[0];
             final double v1 = splzi[1];
             final double v2 = splzi[2];
             final double v3 = splzi[3];
             tuv000 = fma(tu00, v0, tuv000);
             tuv100 = fma(tu10, v0, tuv100);
             tuv010 = fma(tu01, v0, tuv010);
             tuv001 = fma(tu00, v1, tuv001);
             tuv200 = fma(tu20, v0, tuv200);
             tuv020 = fma(tu02, v0, tuv020);
             tuv002 = fma(tu00, v2, tuv002);
             tuv110 = fma(tu11, v0, tuv110);
             tuv101 = fma(tu10, v1, tuv101);
             tuv011 = fma(tu01, v1, tuv011);
             tuv300 = fma(tu30, v0, tuv300);
             tuv030 = fma(tu03, v0, tuv030);
             tuv003 = fma(tu00, v3, tuv003);
             tuv210 = fma(tu21, v0, tuv210);
             tuv201 = fma(tu20, v1, tuv201);
             tuv120 = fma(tu12, v0, tuv120);
             tuv021 = fma(tu02, v1, tuv021);
             tuv102 = fma(tu10, v2, tuv102);
             tuv012 = fma(tu01, v2, tuv012);
             tuv111 = fma(tu11, v1, tuv111);
           }
           double[] out = fracPermPhi[n];
           out[t000] = tuv000;
           out[t100] = tuv100;
           out[t010] = tuv010;
           out[t001] = tuv001;
           out[t200] = tuv200;
           out[t020] = tuv020;
           out[t002] = tuv002;
           out[t110] = tuv110;
           out[t101] = tuv101;
           out[t011] = tuv011;
           out[t300] = tuv300;
           out[t030] = tuv030;
           out[t003] = tuv003;
           out[t210] = tuv210;
           out[t201] = tuv201;
           out[t120] = tuv120;
           out[t021] = tuv021;
           out[t102] = tuv102;
           out[t012] = tuv012;
           out[t111] = tuv111;
           double[] in = out;
           out = cartPermPhi[n];
           out[0] = transformFieldMatrix[0][0] * in[0];
           for (int j = 1; j < 4; j++) {
             out[j] = 0.0;
             for (int k = 1; k < 4; k++) {
               out[j] = fma(transformFieldMatrix[j][k], in[k], out[j]);
             }
           }
           for (int j = 4; j < 10; j++) {
             out[j] = 0.0;
             for (int k = 4; k < 10; k++) {
               out[j] = fma(transformFieldMatrix[j][k], in[k], out[j]);
             }
           }
         }
       }
 
       @Override
       public IntegerSchedule schedule() {
         return IntegerSchedule.fixed();
       }
 
       @Override
       public void start() {
         int threadIndex = getThreadIndex();
         permanentPhiTime[threadIndex] -= System.nanoTime();
       }
     }
   }
 
   /**
    * This class is used to obtain the reciprocal space potential and fields due to induced dipoles
    * from the PME grid.
    *
    * <p>An external ParallelRegion can be used as follows: <code>
    * start() { inducedPhiRegion.setCartInducedDipolePhi(...); }
    * <p>
    * run() { execute(0, nAtoms - 1, inducedPhiLoops[threadID]); }
    * </code>
    */
   private class InducedPhiRegion extends ParallelRegion {
 
     final InducedPhiLoop[] inducedPhiLoops;
 
     private final BSplineRegion bSplineRegion;
     private double[][] cartInducedDipolePhi;
     private double[][] cartInducedDipolePhiCR;
     private double[][] fracInducedDipolePhi;
     private double[][] fracInducedDipolePhiCR;
 
     InducedPhiRegion(BSplineRegion bSplineRegion) {
       this.bSplineRegion = bSplineRegion;
       inducedPhiLoops = new InducedPhiLoop[threadCount];
       for (int i = 0; i < threadCount; i++) {
         inducedPhiLoops[i] = new InducedPhiLoop();
       }
     }
 
     @Override
     public void run() {
       try {
         int threadID = getThreadIndex();
         execute(0, nAtoms - 1, inducedPhiLoops[threadID]);
       } catch (Exception e) {
         logger.severe(e.toString());
       }
     }
 
     void setInducedDipolePhi(
         double[][] cartInducedDipolePhi,
         double[][] cartInducedDipolePhiCR,
         double[][] fracInducedDipolePhi,
         double[][] fracInducedDipolePhiCR) {
       this.cartInducedDipolePhi = cartInducedDipolePhi;
       this.cartInducedDipolePhiCR = cartInducedDipolePhiCR;
       this.fracInducedDipolePhi = fracInducedDipolePhi;
       this.fracInducedDipolePhiCR = fracInducedDipolePhiCR;
     }
 
     public class InducedPhiLoop extends IntegerForLoop {
 
       @Override
       public void finish() {
         int threadIndex = getThreadIndex();
         inducedPhiTime[threadIndex] += System.nanoTime();
       }
 
       @Override
       public void run(int lb, int ub) {
         for (int n = lb; n <= ub; n++) {
           final double[][] splx = bSplineRegion.splineX[0][n];
           final double[][] sply = bSplineRegion.splineY[0][n];
           final double[][] splz = bSplineRegion.splineZ[0][n];
           final int[] igrd = bSplineRegion.initGrid[0][n];
           final int igrd0 = igrd[0];
           final int jgrd0 = igrd[1];
           int k0 = igrd[2];
           double tuv000 = 0.0;
           double tuv100 = 0.0;
           double tuv010 = 0.0;
           double tuv001 = 0.0;
           double tuv200 = 0.0;
           double tuv020 = 0.0;
           double tuv002 = 0.0;
           double tuv110 = 0.0;
           double tuv101 = 0.0;
           double tuv011 = 0.0;
           double tuv300 = 0.0;
           double tuv030 = 0.0;
           double tuv003 = 0.0;
           double tuv210 = 0.0;
           double tuv201 = 0.0;
           double tuv120 = 0.0;
           double tuv021 = 0.0;
           double tuv102 = 0.0;
           double tuv012 = 0.0;
           double tuv111 = 0.0;
           double tuv000p = 0.0;
           double tuv100p = 0.0;
           double tuv010p = 0.0;
           double tuv001p = 0.0;
           double tuv200p = 0.0;
           double tuv020p = 0.0;
           double tuv002p = 0.0;
           double tuv110p = 0.0;
           double tuv101p = 0.0;
           double tuv011p = 0.0;
           double tuv300p = 0.0;
           double tuv030p = 0.0;
           double tuv003p = 0.0;
           double tuv210p = 0.0;
           double tuv201p = 0.0;
           double tuv120p = 0.0;
           double tuv021p = 0.0;
           double tuv102p = 0.0;
           double tuv012p = 0.0;
           double tuv111p = 0.0;
           for (int ith3 = 0; ith3 < bSplineOrder; ith3++) {
             final int k = mod(++k0, fftZ);
             int j0 = jgrd0;
             double tu00 = 0.0;
             double tu10 = 0.0;
             double tu01 = 0.0;
             double tu20 = 0.0;
             double tu11 = 0.0;
             double tu02 = 0.0;
             double tu30 = 0.0;
             double tu21 = 0.0;
             double tu12 = 0.0;
             double tu03 = 0.0;
             double tu00p = 0.0;
             double tu10p = 0.0;
             double tu01p = 0.0;
             double tu20p = 0.0;
             double tu11p = 0.0;
             double tu02p = 0.0;
             double tu30p = 0.0;
             double tu21p = 0.0;
             double tu12p = 0.0;
             double tu03p = 0.0;
             for (int ith2 = 0; ith2 < bSplineOrder; ith2++) {
               final int j = mod(++j0, fftY);
               int i0 = igrd0;
               double t0 = 0.0;
               double t1 = 0.0;
               double t2 = 0.0;
               double t3 = 0.0;
               double t0p = 0.0;
               double t1p = 0.0;
               double t2p = 0.0;
               double t3p = 0.0;
               for (int ith1 = 0; ith1 < bSplineOrder; ith1++) {
                 final int i = mod(++i0, fftX);
                 final int ii = interleavedIndex(i, j, k, fftX, fftY);
                 final double tq = splineBuffer.get(ii);
                 final double tp = splineBuffer.get(ii + 1);
                 final double[] splxi = splx[ith1];
                 final double s0 = splxi[0];
                 final double s1 = splxi[1];
                 final double s2 = splxi[2];
                 final double s3 = splxi[3];
                 t0 = fma(tq, s0, t0);
                 t1 = fma(tq, s1, t1);
                 t2 = fma(tq, s2, t2);
                 t3 = fma(tq, s3, t3);
                 t0p = fma(tp, s0, t0p);
                 t1p = fma(tp, s1, t1p);
                 t2p = fma(tp, s2, t2p);
                 t3p = fma(tp, s3, t3p);
               }
               final double[] splyi = sply[ith2];
               final double u0 = splyi[0];
               final double u1 = splyi[1];
               final double u2 = splyi[2];
               final double u3 = splyi[3];
               tu00 = fma(t0, u0, tu00);
               tu10 = fma(t1, u0, tu10);
               tu01 = fma(t0, u1, tu01);
               tu20 = fma(t2, u0, tu20);
               tu11 = fma(t1, u1, tu11);
               tu02 = fma(t0, u2, tu02);
               tu30 = fma(t3, u0, tu30);
               tu21 = fma(t2, u1, tu21);
               tu12 = fma(t1, u2, tu12);
               tu03 = fma(t0, u3, tu03);
               tu00p = fma(t0p, u0, tu00p);
               tu10p = fma(t1p, u0, tu10p);
               tu01p = fma(t0p, u1, tu01p);
               tu20p = fma(t2p, u0, tu20p);
               tu11p = fma(t1p, u1, tu11p);
               tu02p = fma(t0p, u2, tu02p);
               tu30p = fma(t3p, u0, tu30p);
               tu21p = fma(t2p, u1, tu21p);
               tu12p = fma(t1p, u2, tu12p);
               tu03p = fma(t0p, u3, tu03p);
             }
             final double[] splzi = splz[ith3];
             final double v0 = splzi[0];
             final double v1 = splzi[1];
             final double v2 = splzi[2];
             final double v3 = splzi[3];
             tuv000 = fma(tu00, v0, tuv000);
             tuv100 = fma(tu10, v0, tuv100);
             tuv010 = fma(tu01, v0, tuv010);
             tuv001 = fma(tu00, v1, tuv001);
             tuv200 = fma(tu20, v0, tuv200);
             tuv020 = fma(tu02, v0, tuv020);
             tuv002 = fma(tu00, v2, tuv002);
             tuv110 = fma(tu11, v0, tuv110);
             tuv101 = fma(tu10, v1, tuv101);
             tuv011 = fma(tu01, v1, tuv011);
             tuv300 = fma(tu30, v0, tuv300);
             tuv030 = fma(tu03, v0, tuv030);
             tuv003 = fma(tu00, v3, tuv003);
             tuv210 = fma(tu21, v0, tuv210);
             tuv201 = fma(tu20, v1, tuv201);
             tuv120 = fma(tu12, v0, tuv120);
             tuv021 = fma(tu02, v1, tuv021);
             tuv102 = fma(tu10, v2, tuv102);
             tuv012 = fma(tu01, v2, tuv012);
             tuv111 = fma(tu11, v1, tuv111);
             tuv000p = fma(tu00p, v0, tuv000p);
             tuv100p = fma(tu10p, v0, tuv100p);
             tuv010p = fma(tu01p, v0, tuv010p);
             tuv001p = fma(tu00p, v1, tuv001p);
             tuv200p = fma(tu20p, v0, tuv200p);
             tuv020p = fma(tu02p, v0, tuv020p);
             tuv002p = fma(tu00p, v2, tuv002p);
             tuv110p = fma(tu11p, v0, tuv110p);
             tuv101p = fma(tu10p, v1, tuv101p);
             tuv011p = fma(tu01p, v1, tuv011p);
             tuv300p = fma(tu30p, v0, tuv300p);
             tuv030p = fma(tu03p, v0, tuv030p);
             tuv003p = fma(tu00p, v3, tuv003p);
             tuv210p = fma(tu21p, v0, tuv210p);
             tuv201p = fma(tu20p, v1, tuv201p);
             tuv120p = fma(tu12p, v0, tuv120p);
             tuv021p = fma(tu02p, v1, tuv021p);
             tuv102p = fma(tu10p, v2, tuv102p);
             tuv012p = fma(tu01p, v2, tuv012p);
             tuv111p = fma(tu11p, v1, tuv111p);
           }
           double[] out = fracInducedDipolePhi[n];
           out[t000] = tuv000;
           out[t100] = tuv100;
           out[t010] = tuv010;
           out[t001] = tuv001;
           out[t200] = tuv200;
           out[t020] = tuv020;
           out[t002] = tuv002;
           out[t110] = tuv110;
           out[t101] = tuv101;
           out[t011] = tuv011;
           out[t300] = tuv300;
           out[t030] = tuv030;
           out[t003] = tuv003;
           out[t210] = tuv210;
           out[t201] = tuv201;
           out[t120] = tuv120;
           out[t021] = tuv021;
           out[t102] = tuv102;
           out[t012] = tuv012;
           out[t111] = tuv111;
           double[] in = out;
           out = cartInducedDipolePhi[n];
           out[0] = transformFieldMatrix[0][0] * in[0];
           for (int j = 1; j < 4; j++) {
             out[j] = 0.0;
             for (int k = 1; k < 4; k++) {
               out[j] = fma(transformFieldMatrix[j][k], in[k], out[j]);
             }
           }
           for (int j = 4; j < 10; j++) {
             out[j] = 0.0;
             for (int k = 4; k < 10; k++) {
               out[j] = fma(transformFieldMatrix[j][k], in[k], out[j]);
             }
           }
 
           out = fracInducedDipolePhiCR[n];
           out[t000] = tuv000p;
           out[t100] = tuv100p;
           out[t010] = tuv010p;
           out[t001] = tuv001p;
           out[t200] = tuv200p;
           out[t020] = tuv020p;
           out[t002] = tuv002p;
           out[t110] = tuv110p;
           out[t101] = tuv101p;
           out[t011] = tuv011p;
           out[t300] = tuv300p;
           out[t030] = tuv030p;
           out[t003] = tuv003p;
           out[t210] = tuv210p;
           out[t201] = tuv201p;
           out[t120] = tuv120p;
           out[t021] = tuv021p;
           out[t102] = tuv102p;
           out[t012] = tuv012p;
           out[t111] = tuv111p;
           in = out;
           out = cartInducedDipolePhiCR[n];
           out[0] = transformFieldMatrix[0][0] * in[0];
           for (int j = 1; j < 4; j++) {
             out[j] = 0.0;
             for (int k = 1; k < 4; k++) {
               out[j] = fma(transformFieldMatrix[j][k], in[k], out[j]);
             }
           }
           for (int j = 4; j < 10; j++) {
             out[j] = 0.0;
             for (int k = 4; k < 10; k++) {
               out[j] = fma(transformFieldMatrix[j][k], in[k], out[j]);
             }
           }
         }
       }
 
       @Override
       public IntegerSchedule schedule() {
         return IntegerSchedule.fixed();
       }
 
       @Override
       public void start() {
         int threadIndex = getThreadIndex();
         inducedPhiTime[threadIndex] -= System.nanoTime();
       }
     }
   }
 
   private class FractionalMultipoleRegion extends ParallelRegion {
 
     private double[][][] globalMultipoles = null;
     private double[][][] fracMultipoles = null;
     private boolean[] use = null;
     private FractionalMultipoleLoop[] fractionalMultipoleLoops;
 
     @Override
     public void start() {
       if (fractionalMultipoleLoops == null) {
         int nThreads = getThreadCount();
         fractionalMultipoleLoops = new FractionalMultipoleLoop[nThreads];
         for (int i = 0; i < nThreads; i++) {
           fractionalMultipoleLoops[i] = new FractionalMultipoleLoop();
         }
       }
     }
 
     void setPermanent(double[][][] globalMultipoles, double[][][] fracMultipoles) {
       this.globalMultipoles = globalMultipoles;
       this.fracMultipoles = fracMultipoles;
     }
 
     private void setUse(boolean[] use) {
       this.use = use;
     }
 
     @Override
     public void run() {
       int threadIndex = getThreadIndex();
       try {
         execute(0, nAtoms - 1, fractionalMultipoleLoops[threadIndex]);
       } catch (Exception e) {
         throw new RuntimeException(e);
       }
     }
 
     private class FractionalMultipoleLoop extends IntegerForLoop {
 
       @Override
       public void run(int lb, int ub) {
         for (int s = 0; s < nSymm; s++) {
           for (int i = lb; i <= ub; i++) {
             if (use[i]) {
               toFractionalMultipole(globalMultipoles[s][i], fracMultipoles[s][i]);
             }
           }
         }
       }
 
       @Override
       public IntegerSchedule schedule() {
         return IntegerSchedule.fixed();
       }
     }
 
   }
 
   private class FractionalInducedRegion extends ParallelRegion {
 
     private double[][][] inducedDipole;
     private double[][][] inducedDipoleCR;
     private double[][][] inducedDipoleFrac;
     private double[][][] inducedDipoleFracCR;
     private boolean[] use = null;
     private FractionalInducedLoop[] fractionalInducedLoops;
 
     @Override
     public void start() {
       if (fractionalInducedLoops == null) {
         int nThreads = getThreadCount();
         fractionalInducedLoops = new FractionalInducedLoop[nThreads];
         for (int i = 0; i < nThreads; i++) {
           fractionalInducedLoops[i] = new FractionalInducedLoop();
         }
       }
     }
 
     void setInducedDipoles(double[][][] inducedDipole, double[][][] inducedDipoleCR,
                            double[][][] inducedDipoleFrac, double[][][] inducedDipoleFracCR) {
       this.inducedDipole = inducedDipole;
       this.inducedDipoleCR = inducedDipoleCR;
       this.inducedDipoleFrac = inducedDipoleFrac;
       this.inducedDipoleFracCR = inducedDipoleFracCR;
     }
 
     private void setUse(boolean[] use) {
       this.use = use;
     }
 
     @Override
     public void run() {
       int threadIndex = getThreadIndex();
       try {
         execute(0, nAtoms - 1, fractionalInducedLoops[threadIndex]);
       } catch (Exception e) {
         throw new RuntimeException(e);
       }
     }
 
     private class FractionalInducedLoop extends IntegerForLoop {
 
       @Override
       public void run(int lb, int ub) {
         for (int s = 0; s < nSymm; s++) {
           for (int i = lb; i <= ub; i++) {
             if (use[i]) {
               toFractionalDipole(inducedDipole[s][i], inducedDipoleFrac[s][i]);
               toFractionalDipole(inducedDipoleCR[s][i], inducedDipoleFracCR[s][i]);
             }
           }
         }
       }
 
       @Override
       public IntegerSchedule schedule() {
         return IntegerSchedule.fixed();
       }
     }
 
   }
 }