// ******************************************************************************
   //
   // 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.realspace;
  
  import edu.rit.pj.IntegerForLoop;
  import edu.rit.pj.ParallelRegion;
  import edu.rit.pj.ParallelTeam;
  import edu.rit.pj.reduction.SharedDouble;
  import ffx.crystal.Crystal;
  import ffx.numerics.atomic.AtomicDoubleArray.AtomicDoubleArrayImpl;
  import ffx.numerics.atomic.AtomicDoubleArray3D;
  import ffx.numerics.spline.TriCubicSpline;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.Utilities;
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.Molecule;
  import ffx.potential.bonded.Residue;
  import ffx.realspace.parsers.RealSpaceFile;
  import ffx.xray.DataContainer;
  import ffx.xray.DiffractionData;
  import ffx.xray.RefinementMinimize.RefinementMode;
  import ffx.xray.RefinementModel;
  import org.apache.commons.configuration2.CompositeConfiguration;
  
  import java.util.List;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  import static ffx.numerics.math.ScalarMath.mod;
  import static java.lang.String.format;
  import static java.util.Arrays.fill;
  import static org.apache.commons.math3.util.FastMath.floor;
  
  /**
   * RealSpaceData class.
   *
   * @author Timothy D. Fenn
   * @since 1.0
   */
  public class RealSpaceData implements DataContainer {
  
    private static final Logger logger = Logger.getLogger(RealSpaceData.class.getName());
    /**
     * Parallel Team instance.
     */
    private final ParallelTeam parallelTeam;
    /**
     * Calculate the real space target in parallel.
     */
    private final RealSpaceRegion realSpaceRegion;
    /**
     * The real space data files.
     */
    private final RealSpaceFile[] realSpaceFile;
    /**
     * The number of real space data sources to consider.
     */
    private final int nRealSpaceData;
    /**
     * The refinement model.
     */
    private final RefinementModel refinementModel;
    /**
     * A flag to indicate if the lambda term is active.
    */
   private final boolean lambdaTerm;
   /**
    * The collection of MolecularAssembly instances that model the real space data.
    */
   private final MolecularAssembly[] molecularAssemblies;
   /**
    * The collection of crystals that describe the PBC and symmetry of each data source.
    */
   private Crystal[] crystal;
   /**
    * The real space refinement data for each data source.
    */
   private RealSpaceRefinementData[] refinementData;
   /**
    * The total real space energy.
    */
   private double realSpaceEnergy = 0.0;
   /**
    * The partial derivative of the real space energy with respect to lambda.
    */
   private double realSpacedUdL = 0.0;
   /**
    * The real space gradient.
    */
   private double[] realSpaceGradient;
   /**
    * The partial derivative of the real space gradient with respect to lambda.
    */
   private double[] realSpacedUdXdL;
   /**
    * The weight of the data relative to the weight of the force field.
    */
   private double xweight;
   /**
    * The current value of the state variable lambda.
    */
   private double lambda = 1.0;
 
   /**
    * Construct a real space data molecularAssemblies, assumes a real space map with a weight of 1.0
    * using the same name as the molecular molecularAssemblies.
    *
    * @param molecularAssembly {@link ffx.potential.MolecularAssembly molecular molecularAssemblies}
    *                          object, used as the atomic model for comparison against the data
    * @param properties        system properties file
    * @param parallelTeam      a {@link edu.rit.pj.ParallelTeam} object.
    * @param diffractionData   {@link ffx.xray.DiffractionData diffraction data}
    */
   public RealSpaceData(
       MolecularAssembly molecularAssembly,
       CompositeConfiguration properties,
       ParallelTeam parallelTeam,
       DiffractionData diffractionData) {
     this(new MolecularAssembly[]{molecularAssembly}, properties, parallelTeam, diffractionData);
   }
 
   /**
    * Construct a real space data molecularAssemblies, assumes a real space map with a weight of 1.0
    * using the same name as the molecularAssemblies.
    *
    * @param molecularAssemblies {@link ffx.potential.MolecularAssembly molecular
    *                            molecularAssemblies} object, used as the atomic model for comparison against the data
    * @param properties          system properties file
    * @param parallelTeam        a {@link edu.rit.pj.ParallelTeam} object.
    * @param diffractionData     {@link ffx.xray.DiffractionData diffraction data}
    */
   public RealSpaceData(
       MolecularAssembly[] molecularAssemblies,
       CompositeConfiguration properties,
       ParallelTeam parallelTeam,
       DiffractionData diffractionData) {
     this.molecularAssemblies = molecularAssemblies;
     this.parallelTeam = parallelTeam;
     this.realSpaceFile = null;
     this.nRealSpaceData = 1;
     crystal = new Crystal[nRealSpaceData];
     crystal[0] = diffractionData.getCrystal()[0];
     refinementData = new RealSpaceRefinementData[nRealSpaceData];
     refinementData[0] = new RealSpaceRefinementData();
     refinementData[0].setPeriodic(true);
 
     xweight = properties.getDouble("xweight", 1.0);
     lambdaTerm = properties.getBoolean("lambdaterm", false);
 
     if (logger.isLoggable(Level.INFO)) {
       StringBuilder sb = new StringBuilder(" Real Space Refinement Settings\n");
       sb.append(format("  Refinement weight (xweight): %5.3f", xweight));
       logger.info(sb.toString());
     }
 
     if (!diffractionData.getScaled()[0]) {
       diffractionData.scaleBulkFit();
       diffractionData.printStats();
     }
 
     // get Fo-Fc difference density
     diffractionData.getCrystalReciprocalSpacesFc()[0].computeAtomicGradients(
         diffractionData.getRefinementData()[0].foFc1,
         diffractionData.getRefinementData()[0].freeR,
         diffractionData.getRefinementData()[0].rFreeFlag,
         RefinementMode.COORDINATES);
 
     refinementData[0].setOrigin(0, 0, 0);
     int extx = (int) diffractionData.getCrystalReciprocalSpacesFc()[0].getXDim();
     int exty = (int) diffractionData.getCrystalReciprocalSpacesFc()[0].getYDim();
     int extz = (int) diffractionData.getCrystalReciprocalSpacesFc()[0].getZDim();
     refinementData[0].setExtent(extx, exty, extz);
     refinementData[0].setNI(extx, exty, extz);
     refinementData[0].setData(new double[extx * exty * extz]);
     for (int k = 0; k < extz; k++) {
       for (int j = 0; j < exty; j++) {
         for (int i = 0; i < extx; i++) {
           int index1 = (i + extx * (j + exty * k));
           int index2 = 2 * index1;
           refinementData[0].getData()[index1] =
               diffractionData.getCrystalReciprocalSpacesFc()[0].getDensityGrid()[index2];
         }
       }
     }
 
     // Initialize the refinement model.
     refinementModel = new RefinementModel(molecularAssemblies);
 
     // Initialize the RealSpaceRegion.
     int nAtoms = refinementModel.getTotalAtomArray().length;
     realSpaceRegion =
         new RealSpaceRegion(parallelTeam.getThreadCount(), nAtoms, refinementData.length);
   }
 
   /**
    * Construct a real space data molecularAssemblies, assumes a real space map with a weight of 1.0
    * using the same name as the molecular molecularAssemblies.
    *
    * @param assembly     {@link ffx.potential.MolecularAssembly molecular molecularAssemblies} object,
    *                     used as the atomic model for comparison against the data
    * @param properties   system properties file
    * @param parallelTeam a {@link edu.rit.pj.ParallelTeam} object.
    */
   public RealSpaceData(
       MolecularAssembly assembly, CompositeConfiguration properties, ParallelTeam parallelTeam) {
     this(new MolecularAssembly[]{assembly}, properties, parallelTeam, new RealSpaceFile(assembly));
   }
 
   /**
    * Construct a real space data molecularAssemblies.
    *
    * @param assembly     {@link ffx.potential.MolecularAssembly molecular molecularAssemblies} object,
    *                     used as the atomic model for comparison against the data
    * @param properties   system properties file
    * @param parallelTeam a {@link edu.rit.pj.ParallelTeam} object.
    * @param datafile     one or more {@link ffx.realspace.parsers.RealSpaceFile} to be refined against
    */
   public RealSpaceData(
       MolecularAssembly assembly,
       CompositeConfiguration properties,
       ParallelTeam parallelTeam,
       RealSpaceFile... datafile) {
     this(new MolecularAssembly[]{assembly}, properties, parallelTeam, datafile);
   }
 
   /**
    * Construct a real space data molecularAssemblies.
    *
    * @param molecularAssemblies {@link ffx.potential.MolecularAssembly molecular
    *                            molecularAssemblies} object array (typically containing alternate conformer assemblies),
    *                            used as the atomic model for comparison against the data
    * @param properties          system properties file
    * @param parallelTeam        a {@link edu.rit.pj.ParallelTeam} object.
    * @param dataFile            one or more {@link ffx.realspace.parsers.RealSpaceFile} to be refined against
    */
   public RealSpaceData(
       MolecularAssembly[] molecularAssemblies,
       CompositeConfiguration properties,
       ParallelTeam parallelTeam,
       RealSpaceFile... dataFile) {
 
     this.molecularAssemblies = molecularAssemblies;
     this.parallelTeam = parallelTeam;
     this.realSpaceFile = dataFile;
     this.nRealSpaceData = dataFile.length;
     crystal = new Crystal[nRealSpaceData];
     refinementData = new RealSpaceRefinementData[nRealSpaceData];
 
     xweight = properties.getDouble("xweight", 1.0);
     lambdaTerm = properties.getBoolean("lambdaterm", false);
 
     for (int i = 0; i < nRealSpaceData; i++) {
       crystal[i] =
           dataFile[i].getRealSpaceFileFilter().getCrystal(dataFile[i].getFilename(), properties);
       if (crystal[i] == null) {
         logger.severe(" CCP4 map file does not contain full crystal information!");
       }
     }
 
     for (int i = 0; i < nRealSpaceData; i++) {
       refinementData[i] = new RealSpaceRefinementData();
       dataFile[i]
           .getRealSpaceFileFilter()
           .readFile(dataFile[i].getFilename(), refinementData[i], properties);
 
       if (refinementData[i].getOrigin()[0] == 0
           && refinementData[i].getOrigin()[1] == 0
           && refinementData[i].getOrigin()[2] == 0
           && refinementData[i].getExtent()[0] == refinementData[i].getNi()[0]
           && refinementData[i].getExtent()[1] == refinementData[i].getNi()[1]
           && refinementData[i].getExtent()[2] == refinementData[i].getNi()[2]) {
         refinementData[i].setPeriodic(true);
       }
     }
 
     if (logger.isLoggable(Level.INFO)) {
       StringBuilder sb = new StringBuilder(" Real Space Refinement Settings\n");
       sb.append(format("  Refinement weight (xweight): %5.3f", xweight));
       logger.info(sb.toString());
     }
 
     // now set up the refinement model
     refinementModel = new RefinementModel(molecularAssemblies);
 
     // Initialize the RealSpaceRegion.
     int nAtoms = refinementModel.getTotalAtomArray().length;
     realSpaceRegion =
         new RealSpaceRegion(parallelTeam.getThreadCount(), nAtoms, refinementData.length);
   }
 
   /**
    * Similar to Potential.destroy(), frees up resources associated with this RealSpaceData.
    *
    * @return If assets successfully freed.
    */
   public boolean destroy() {
     try {
       boolean underlyingShutdown = true;
       for (MolecularAssembly assembly : molecularAssemblies) {
         // Continue trying to shut assemblies down even if one fails to shut down.
         boolean thisShutdown = assembly.destroy();
         underlyingShutdown = underlyingShutdown && thisShutdown;
       }
       parallelTeam.shutdown();
       return underlyingShutdown;
     } catch (Exception ex) {
       logger.warning(format(" Exception in shutting down a RealSpaceData: %s", ex));
       logger.info(Utilities.stackTraceToString(ex));
       return false;
     }
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public Atom[] getActiveAtomArray() {
     return refinementModel.getActiveAtomArray();
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public List<List<Molecule>> getAltMolecules() {
     return refinementModel.getAltMolecules();
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public List<List<Residue>> getAltResidues() {
     return refinementModel.getAltResidues();
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public Atom[] getAtomArray() {
     return refinementModel.getTotalAtomArray();
   }
 
   /**
    * Getter for the field <code>crystal</code>.
    *
    * @return the crystal
    */
   public Crystal[] getCrystal() {
     return crystal;
   }
 
   /**
    * Setter for the field <code>crystal</code>.
    *
    * @param crystal the crystal to set
    */
   public void setCrystal(Crystal[] crystal) {
     this.crystal = crystal;
   }
 
   /**
    * Getter for the field <code>lambda</code>.
    *
    * @return the lambda
    */
   public double getLambda() {
     return lambda;
   }
 
   /**
    * Set the current value of the state variable.
    *
    * @param lambda a double.
    */
   public void setLambda(double lambda) {
     this.lambda = lambda;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public MolecularAssembly[] getMolecularAssemblies() {
     return molecularAssemblies;
   }
 
   /**
    * Getter for the field <code>realSpaceGradient</code>.
    *
    * @param gradient the gradient array.
    * @return the real space gradient added to the input gradient array, or a new array if the
    * gradient is null or too small.
    */
   public double[] getRealSpaceGradient(double[] gradient) {
     int nAtoms = refinementModel.getTotalAtomArray().length;
     int nActiveAtoms = 0;
     for (int i = 0; i < nAtoms; i++) {
       if (refinementModel.getTotalAtomArray()[i].isActive()) {
         nActiveAtoms++;
       }
     }
 
     if (gradient == null || gradient.length < nActiveAtoms * 3) {
       gradient = new double[nActiveAtoms * 3];
     }
     for (int i = 0; i < nActiveAtoms * 3; i++) {
       gradient[i] += realSpaceGradient[i];
     }
     return gradient;
   }
 
   /**
    * Getter for the field <code>refinementData</code>.
    *
    * @return the refinementData
    */
   public RealSpaceRefinementData[] getRefinementData() {
     return refinementData;
   }
 
   /**
    * Setter for the field <code>refinementData</code>.
    *
    * @param refinementData the refinementData to set
    */
   public void setRefinementData(RealSpaceRefinementData[] refinementData) {
     this.refinementData = refinementData;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public RefinementModel getRefinementModel() {
     return refinementModel;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double getWeight() {
     return xweight;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void setWeight(double weight) {
     this.xweight = weight;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public String printEnergyUpdate() {
     StringBuilder sb = new StringBuilder();
     for (int i = 0; i < nRealSpaceData; i++) {
       sb.append(
           format(
               "     dataset %d (weight: %5.1f): chemical energy: %8.2f density score: %8.2f\n",
               i + 1,
               realSpaceFile[i].getWeight(),
               molecularAssemblies[0].getPotentialEnergy().getTotalEnergy(),
               realSpaceFile[i].getWeight() * refinementData[i].getDensityScore()));
     }
     return sb.toString();
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public String printOptimizationHeader() {
     return "Density score";
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public String printOptimizationUpdate() {
     StringBuilder sb = new StringBuilder();
     for (int i = 0; i < nRealSpaceData; i++) {
       sb.append(format("%6.2f ", refinementData[i].getDensityScore()));
     }
     return sb.toString();
   }
 
   /**
    * compute real space target value, also fills in atomic derivatives
    *
    * @return target value sum over all data sets.
    */
   double computeRealSpaceTarget() {
 
     long time = -System.nanoTime();
     // Zero out the realSpaceTarget energy.
     realSpaceEnergy = 0.0;
     // Zero out the realSpacedUdL energy.
     realSpacedUdL = 0.0;
     // Initialize gradient to zero; allocate space if necessary.
     int nActive = 0;
     int nAtoms = refinementModel.getTotalAtomArray().length;
     for (int i = 0; i < nAtoms; i++) {
       if (refinementModel.getTotalAtomArray()[i].isActive()) {
         nActive++;
       }
     }
 
     int nGrad = nActive * 3;
     if (realSpaceGradient == null || realSpaceGradient.length < nGrad) {
       realSpaceGradient = new double[nGrad];
     } else {
       fill(realSpaceGradient, 0.0);
     }
 
     // Initialize dUdXdL to zero; allocate space if necessary.
     if (realSpacedUdXdL == null || realSpacedUdXdL.length < nGrad) {
       realSpacedUdXdL = new double[nGrad];
     } else {
       fill(realSpacedUdXdL, 0.0);
     }
 
     try {
       parallelTeam.execute(realSpaceRegion);
     } catch (Exception e) {
       String message = " Exception computing real space energy";
       logger.log(Level.SEVERE, message, e);
     }
 
     time += System.nanoTime();
     if (logger.isLoggable(Level.FINE)) {
       logger.fine(format(" Real space energy time: %16.8f (sec).", time * 1.0e-9));
     }
 
     return realSpaceEnergy;
   }
 
   /**
    * getdEdL.
    *
    * @return a double.
    */
   double getdEdL() {
     return realSpacedUdL;
   }
 
   /**
    * getdEdXdL.
    *
    * @param gradient an array of {@link double} objects.
    * @return an array of {@link double} objects.
    */
   double[] getdEdXdL(double[] gradient) {
     int nAtoms = refinementModel.getTotalAtomArray().length;
     int nActiveAtoms = 0;
     for (int i = 0; i < nAtoms; i++) {
       if (refinementModel.getTotalAtomArray()[i].isActive()) {
         nActiveAtoms++;
       }
     }
 
     if (gradient == null || gradient.length < nActiveAtoms * 3) {
       gradient = new double[nActiveAtoms * 3];
     }
 
     for (int i = 0; i < nActiveAtoms * 3; i++) {
       gradient[i] += realSpacedUdXdL[i];
     }
     return gradient;
   }
 
   /**
    * Getter for the field <code>realSpaceFile</code>.
    *
    * @return the realSpaceFile
    */
   private RealSpaceFile[] getRealSpaceFile() {
     return realSpaceFile;
   }
 
   /**
    * Getter for the field <code>nRealSpaceData</code>.
    *
    * @return the nRealSpaceData
    */
   private int getnRealSpaceData() {
     return nRealSpaceData;
   }
 
   private class RealSpaceRegion extends ParallelRegion {
 
     private final AtomicDoubleArray3D gradient;
     private final AtomicDoubleArray3D lambdaGrad;
     private final InitializationLoop[] initializationLoops;
     private final RealSpaceLoop[] realSpaceLoops;
     private final SharedDouble[] sharedTarget;
     private final SharedDouble shareddUdL;
     private final int nAtoms;
     private final int nData;
 
     RealSpaceRegion(int nThreads, int nAtoms, int nData) {
       this.nAtoms = nAtoms;
       this.nData = nData;
       initializationLoops = new InitializationLoop[nThreads];
       realSpaceLoops = new RealSpaceLoop[nThreads];
       sharedTarget = new SharedDouble[nData];
       for (int i = 0; i < nData; i++) {
         sharedTarget[i] = new SharedDouble();
       }
       shareddUdL = new SharedDouble();
       gradient = new AtomicDoubleArray3D(AtomicDoubleArrayImpl.MULTI, nThreads, nAtoms);
       lambdaGrad = new AtomicDoubleArray3D(AtomicDoubleArrayImpl.MULTI, nThreads, nAtoms);
     }
 
     @Override
     public void finish() {
       // Load final values.
       realSpaceEnergy = 0;
       for (int i = 0; i < nData; i++) {
         refinementData[i].setDensityScore(sharedTarget[i].get());
         realSpaceEnergy += getRefinementData()[i].getDensityScore();
       }
       realSpacedUdL = shareddUdL.get();
       int index = 0;
       for (int i = 0; i < nAtoms; i++) {
         Atom atom = refinementModel.getTotalAtomArray()[i];
         if (atom.isActive()) {
           int ii = index * 3;
           double gx = gradient.getX(i);
           double gy = gradient.getY(i);
           double gz = gradient.getZ(i);
           realSpaceGradient[ii] = gx;
           realSpaceGradient[ii + 1] = gy;
           realSpaceGradient[ii + 2] = gz;
           atom.setXYZGradient(gx, gy, gz);
           gx = lambdaGrad.getX(i);
           gy = lambdaGrad.getY(i);
           gz = lambdaGrad.getZ(i);
           realSpacedUdXdL[ii] = gx;
           realSpacedUdXdL[ii + 1] = gy;
           realSpacedUdXdL[ii + 2] = gz;
           atom.setLambdaXYZGradient(gx, gy, gz);
           index++;
         }
       }
     }
 
     @Override
     public void run() throws Exception {
       int threadID = getThreadIndex();
 
       if (initializationLoops[threadID] == null) {
         initializationLoops[threadID] = new InitializationLoop();
       }
       execute(0, nAtoms - 1, initializationLoops[threadID]);
 
       if (realSpaceLoops[threadID] == null) {
         realSpaceLoops[threadID] = new RealSpaceLoop();
       }
       execute(0, nAtoms - 1, realSpaceLoops[threadID]);
     }
 
     @Override
     public void start() {
       for (int i = 0; i < nData; i++) {
         sharedTarget[i].set(0.0);
       }
       shareddUdL.set(0.0);
       gradient.alloc(nAtoms);
       lambdaGrad.alloc(nAtoms);
     }
 
     /**
      * Initialize gradient and lambda gradient arrays.
      */
     private class InitializationLoop extends IntegerForLoop {
 
       @Override
       public void run(int lb, int ub) {
         int threadID = getThreadIndex();
         gradient.reset(threadID, lb, ub);
         lambdaGrad.reset(threadID, lb, ub);
         for (int i = lb; i <= ub; i++) {
           Atom a = refinementModel.getTotalAtomArray()[i];
           a.setXYZGradient(0.0, 0.0, 0.0);
           a.setLambdaXYZGradient(0.0, 0.0, 0.0);
         }
       }
     }
 
     private class RealSpaceLoop extends IntegerForLoop {
 
       double[] target = new double[nData];
       double localdUdL;
 
       @Override
       public void finish() {
         for (int i = 0; i < nData; i++) {
           sharedTarget[i].addAndGet(target[i]);
         }
         shareddUdL.addAndGet(localdUdL);
       }
 
       @Override
       public void run(int first, int last) throws Exception {
 
         int threadID = getThreadIndex();
         double[] xyz = new double[3];
         double[] uvw = new double[3];
         double[] grad = new double[3];
         double[][][] scalar = new double[4][4][4];
         TriCubicSpline spline = new TriCubicSpline();
 
         for (int i = 0; i < getnRealSpaceData(); i++) {
 
           // Define the extent of this real space data sources.
           int extX = getRefinementData()[i].getExtent()[0];
           int extY = getRefinementData()[i].getExtent()[1];
           int extZ = getRefinementData()[i].getExtent()[2];
           int nX = getRefinementData()[i].getNi()[0];
           int nY = getRefinementData()[i].getNi()[1];
           int nZ = getRefinementData()[i].getNi()[2];
           int originX = getRefinementData()[i].getOrigin()[0];
           int originY = getRefinementData()[i].getOrigin()[1];
           int originZ = getRefinementData()[i].getOrigin()[2];
 
           for (int ia = first; ia <= last; ia++) {
             Atom a = refinementModel.getTotalAtomArray()[ia];
             // Only include atoms in the target function that have
             // their use flag set to true and are Active.
             if (!a.getUse()) {
               continue;
             }
 
             double lambdai = 1.0;
             double dUdL = 0.0;
             if (lambdaTerm && a.applyLambda()) {
               lambdai = getLambda();
               dUdL = 1.0;
             }
             a.getXYZ(xyz);
             getCrystal()[i].toFractionalCoordinates(xyz, uvw);
 
             // Logic to find atom in 3d scalar field box.
             final double frx = nX * uvw[0];
             final int ifrx = ((int) floor(frx)) - originX;
             final double dfrx = frx - floor(frx);
 
             final double fry = nY * uvw[1];
             final int ifry = ((int) floor(fry)) - originY;
             final double dfry = fry - floor(fry);
 
             final double frz = nZ * uvw[2];
             final int ifrz = ((int) floor(frz)) - originZ;
             final double dfrz = frz - floor(frz);
 
             if (!refinementData[i].isPeriodic()) {
               if (ifrx - 1 < 0
                   || ifrx + 2 > extX
                   || ifry - 1 < 0
                   || ifry + 2 > extY
                   || ifrz - 1 < 0
                   || ifrz + 2 > extZ) {
                 String message = format(" Atom %s is outside the density will be ignored.", a);
                 logger.warning(message);
                 continue;
               }
             }
 
             // Fill in scalar 4x4 array for interpolation.
             if (getRefinementData()[i].isPeriodic()) {
               for (int ui = ifrx - 1; ui < ifrx + 3; ui++) {
                 int uii = ui - (ifrx - 1);
                 int pui = mod(ui, extX);
                 for (int vi = ifry - 1; vi < ifry + 3; vi++) {
                   int vii = vi - (ifry - 1);
                   int pvi = mod(vi, extY);
                   for (int wi = ifrz - 1; wi < ifrz + 3; wi++) {
                     int wii = wi - (ifrz - 1);
                     int pwi = mod(wi, extZ);
                     scalar[uii][vii][wii] = getRefinementData()[i].getDataIndex(pui, pvi, pwi);
                   }
                 }
               }
             } else {
               for (int ui = ifrx - 1; ui < ifrx + 3; ui++) {
                 int uii = ui - (ifrx - 1);
                 for (int vi = ifry - 1; vi < ifry + 3; vi++) {
                   int vii = vi - (ifry - 1);
                   for (int wi = ifrz - 1; wi < ifrz + 3; wi++) {
                     int wii = wi - (ifrz - 1);
                     scalar[uii][vii][wii] = getRefinementData()[i].getDataIndex(ui, vi, wi);
                   }
                 }
               }
             }
 
             // Scale and interpolate.
             double scale;
             double scaledUdL;
             double atomicWeight = a.getAtomType().atomicWeight;
             if (getRealSpaceFile() != null) {
               atomicWeight *= getRealSpaceFile()[i].getWeight();
             }
             scale = -1.0 * lambdai * atomicWeight;
             scaledUdL = -1.0 * dUdL * atomicWeight;
 
             double val = spline.spline(dfrx, dfry, dfrz, scalar, grad);
             target[i] += scale * val;
             localdUdL += scaledUdL * val;
 
             if (a.isActive()) {
               grad[0] = grad[0] * nX;
               grad[1] = grad[1] * nY;
               grad[2] = grad[2] * nZ;
               // transpose of toFractional
               xyz[0] = grad[0] * getCrystal()[i].A00;
               xyz[1] = grad[0] * getCrystal()[i].A10
                   + grad[1] * getCrystal()[i].A11;
               xyz[2] = grad[0] * getCrystal()[i].A20
                   + grad[1] * getCrystal()[i].A21
                   + grad[2] * getCrystal()[i].A22;
               gradient.add(threadID, ia, scale * xyz[0], scale * xyz[1], scale * xyz[2]);
               lambdaGrad.add(threadID, ia, scaledUdL * xyz[0], scaledUdL * xyz[1], scaledUdL * xyz[2]);
             }
           }
         }
         gradient.reduce(first, last);
         lambdaGrad.reduce(first, last);
       }
 
       @Override
       public void start() {
         for (int i = 0; i < nData; i++) {
           target[i] = 0;
         }
         localdUdL = 0;
       }
     }
   }
 }