// ******************************************************************************
   //
   // 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.bonded;
  
  import ffx.numerics.atomic.AtomicDoubleArray3D;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.parameters.ForceField;
  import org.apache.commons.configuration2.CompositeConfiguration;
  
  import java.util.ArrayList;
  import java.util.List;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  import static ffx.numerics.math.DoubleMath.length;
  import static java.lang.Double.parseDouble;
  import static java.lang.Integer.parseInt;
  import static java.lang.String.format;
  import static java.lang.System.arraycopy;
  import static org.apache.commons.math3.util.FastMath.pow;
  
  /**
   * Restrain the position of atoms to their initial coordinates.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class RestrainPosition extends BondedTerm implements LambdaInterface {
  
    private static final Logger logger = Logger.getLogger(RestrainPosition.class.getName());
  
    private final double[][] equilibriumCoordinates;
  
    /**
     * Force constant variable stores K/2 in Kcal/mol/A. E = K/2 * dx^2.
     */
    private final double forceConstant;
  
    /**
     * Flat bottom radius in Angstroms.
     */
    private final double flatBottom;
  
    private final double[] a1 = new double[3];
    private final double[] dx = new double[3];
    private final double lambdaExp = 1.0;
    private final double[] lambdaGradient;
    private final int nAtoms;
    private final boolean lambdaTerm;
    private double lambda = 1.0;
    private double lambdaPow = pow(lambda, lambdaExp);
    private double dLambdaPow = lambdaExp * pow(lambda, lambdaExp - 1.0);
    private double d2LambdaPow = 0;
    private double dEdL = 0.0;
    private double d2EdL2 = 0.0;
  
    /**
     * Restrain atoms to a position in the global coordinate frame.
     *
     * @param atoms                  The atoms to restrain.
     * @param equilibriumCoordinates The equilibrium coordinates.
     * @param forceConst             The force constant in kcal/mol/A^2.
     * @param flatBottom             The flat bottom radius in Angstroms.
     * @param lambdaTerm             If true, apply lambda to this restraint.
    */
   public RestrainPosition(Atom[] atoms, double[][] equilibriumCoordinates,
                           double forceConst, double flatBottom, boolean lambdaTerm) {
     this.atoms = atoms;
     this.equilibriumCoordinates = equilibriumCoordinates;
     this.forceConstant = forceConst;
     this.flatBottom = flatBottom;
     nAtoms = atoms.length;
     this.lambdaTerm = lambdaTerm;
     if (lambdaTerm) {
       lambdaGradient = new double[nAtoms * 3];
     } else {
       lambdaGradient = null;
       lambda = 1.0;
       lambdaPow = 1.0;
       dLambdaPow = 0.0;
       d2LambdaPow = 0.0;
     }
 
     if (logger.isLoggable(Level.FINE)) {
       logger.info(" RestrainPosition: " + lambdaTerm);
       for (Atom atom : atoms) {
         logger.fine(atom.toString());
       }
     }
   }
 
   /**
    * Returns a copy of the atoms array.
    *
    * @return Copy of the atom array.
    */
   public Atom[] getAtoms() {
     Atom[] retArray = new Atom[nAtoms];
     arraycopy(atoms, 0, retArray, 0, nAtoms);
     return retArray;
   }
 
   /**
    * Returns the force constant in kcal/mol/Angstrom^2.
    *
    * @return a double.
    */
   public double getForceConstant() {
     return forceConstant;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double getLambda() {
     return lambda;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void setLambda(double lambda) {
     if (lambdaTerm) {
       this.lambda = lambda;
       double lambdaWindow = 1.0;
       if (this.lambda <= lambdaWindow) {
         double dldgl = 1.0 / lambdaWindow;
         double l = dldgl * this.lambda;
         double l2 = l * l;
         double l3 = l2 * l;
         double l4 = l2 * l2;
         double l5 = l4 * l;
         double c3 = 10.0;
         double c4 = -15.0;
         double c5 = 6.0;
         double threeC3 = 3.0 * c3;
         double sixC3 = 6.0 * c3;
         double fourC4 = 4.0 * c4;
         double twelveC4 = 12.0 * c4;
         double fiveC5 = 5.0 * c5;
         double twentyC5 = 20.0 * c5;
         lambdaPow = c3 * l3 + c4 * l4 + c5 * l5;
         dLambdaPow = (threeC3 * l2 + fourC4 * l3 + fiveC5 * l4) * dldgl;
         d2LambdaPow = (sixC3 * l + twelveC4 * l2 + twentyC5 * l3) * dldgl * dldgl;
       } else {
         lambdaPow = 1.0;
         dLambdaPow = 0.0;
         d2LambdaPow = 0.0;
       }
     } else {
       this.lambda = 1.0;
       lambdaPow = 1.0;
       dLambdaPow = 0.0;
       d2LambdaPow = 0.0;
     }
   }
 
   /**
    * getNumAtoms.
    *
    * @return a int.
    */
   public int getNumAtoms() {
     return nAtoms;
   }
 
   /**
    * Returns the original coordinates of this restraint, indexed by atoms then x,y,z. This is the
    * opposite order of the internal storage.
    *
    * @return Original coordinates [atoms][xyz]
    */
   public double[][] getEquilibriumCoordinates() {
     double[][] equilibriumCoords = new double[nAtoms][3];
     for (int i = 0; i < nAtoms; i++) {
       for (int j = 0; j < 3; j++) {
         // Mild subtlety here: it is stored internally as [xyz][atoms], but returned as [atoms][xyz]
         equilibriumCoords[i][j] = equilibriumCoordinates[j][i];
       }
     }
     return equilibriumCoords;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double getd2EdL2() {
     if (lambdaTerm) {
       return d2EdL2;
     } else {
       return 0.0;
     }
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double getdEdL() {
     if (lambdaTerm) {
       return dEdL;
     } else {
       return 0.0;
     }
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void getdEdXdL(double[] gradient) {
     if (lambdaTerm) {
       int n3 = nAtoms * 3;
       for (int i = 0; i < n3; i++) {
         gradient[i] += lambdaGradient[i];
       }
     }
   }
 
 
   /**
    * Calculates energy and gradients for this coordinate restraint.
    *
    * @param gradient Calculate gradients
    * @return Energy in the coordinate restraint
    */
   @Override
   public double energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad) {
     double e = 0.0;
     dEdL = 0.0;
     d2EdL2 = 0.0;
     double fx2 = forceConstant * 2.0;
     for (int i = 0; i < nAtoms; i++) {
       // Current atomic coordinates.
       Atom atom = atoms[i];
       // Compute the separation distance.
       atom.getXYZ(a1);
       dx[0] = a1[0] - equilibriumCoordinates[0][i];
       dx[1] = a1[1] - equilibriumCoordinates[1][i];
       dx[2] = a1[2] - equilibriumCoordinates[2][i];
       double r = length(dx);
       double dr = r;
       if (flatBottom > 0.0) {
         dr = Math.max(0.0, r - flatBottom);
       }
       value = dr;
       double dr2 = dr * dr;
       e += dr2;
       if (gradient || lambdaTerm) {
         double scale = fx2 * dr;
         if (r > 0.0) {
           scale /= r;
         }
         final double dedx = dx[0] * scale;
         final double dedy = dx[1] * scale;
         final double dedz = dx[2] * scale;
         final int index = atom.getIndex() - 1;
         if (gradient) {
           grad.add(threadID, index, lambdaPow * dedx, lambdaPow * dedy, lambdaPow * dedz);
         }
         if (lambdaTerm) {
           lambdaGrad.add(threadID, index, dLambdaPow * dedx, dLambdaPow * dedy, dLambdaPow * dedz);
         }
       }
     }
 
     if (lambdaTerm) {
       dEdL = dLambdaPow * forceConstant * e;
       d2EdL2 = d2LambdaPow * forceConstant * e;
     }
 
     energy = forceConstant * e * lambdaPow;
 
     // logger.info(format(" RestrainPosition: %12.6f %12.6f %12.6f", energy, dEdL, d2EdL2));
 
     return energy;
   }
 
   public static RestrainPosition[] parseRestrainPositions(MolecularAssembly molecularAssembly) {
     List<RestrainPosition> restrainPositionList = new ArrayList<>();
     ForceField forceField = molecularAssembly.getForceField();
     CompositeConfiguration properties = forceField.getProperties();
     if (properties.containsKey("restrain-position")) {
       Atom[] atoms = molecularAssembly.getAtomArray();
       String[] lines = properties.getStringArray("restrain-position");
       for (String line : lines) {
         RestrainPosition restrain = parseRestrainPosition(line, atoms, false);
         if (restrain != null) {
           restrainPositionList.add(restrain);
         }
       }
     }
     if (properties.containsKey("restrain-position-lambda")) {
       Atom[] atoms = molecularAssembly.getAtomArray();
       String[] lines = properties.getStringArray("restrain-position-lambda");
       for (String line : lines) {
         RestrainPosition restrain = parseRestrainPosition(line, atoms, true);
         if (restrain != null) {
           restrainPositionList.add(restrain);
         }
       }
     }
 
     if (restrainPositionList.isEmpty()) {
       return null;
     }
 
     return restrainPositionList.toArray(new RestrainPosition[0]);
   }
 
   /**
    * Parse a Restrain-Position line and return a RestrainPosition instance.
    *
    * @param line      The restraint line.
    * @param atoms     The atoms in the system.
    * @param useLambda If true, apply lambda to this restraint.
    * @return A RestrainPosition object.
    */
   public static RestrainPosition parseRestrainPosition(String line, Atom[] atoms, boolean useLambda) {
     String[] tokens = line.split("\\s+");
     if (tokens.length < 1) {
       throw new IllegalArgumentException("Invalid restraint line: " + line);
     }
 
     int nAtoms = atoms.length;
     Atom[] atomArray;
     double[][] coordinates;
     double forceConstant = 50.0;
     double flatBottom = 0.0;
     // First token is the atom index.
     int start = parseInt(tokens[0]);
     if (start < 0) {
       // Range of atoms.
       start = -start - 1;
       int end = parseInt(tokens[1]) - 1;
       if (start >= nAtoms || end < start || end >= nAtoms) {
         logger.severe(format(" Property restrain-position could not be parsed:\n %s.", line));
         return null;
       }
       int n = end - start + 1;
       atomArray = new Atom[n];
       coordinates = new double[3][n];
       for (int j = start, index = 0; j <= end; j++, index++) {
         atomArray[index] = atoms[j];
         coordinates[0][index] = atoms[j].getX();
         coordinates[1][index] = atoms[j].getY();
         coordinates[2][index] = atoms[j].getZ();
       }
       if (tokens.length > 2) {
         forceConstant = parseDouble(tokens[2]);
       }
       if (tokens.length > 3) {
         flatBottom = parseDouble(tokens[3]);
       }
       logger.fine(format(" Restrain-Position of Atoms %d to %d (K=%8.4f, D=%8.4f)",
           start + 1, end + 1, forceConstant, flatBottom));
     } else {
       // Single atom.
       Atom atom = atoms[start - 1];
       atomArray = new Atom[1];
       atomArray[0] = atom;
       double x = atom.getX();
       double y = atom.getY();
       double z = atom.getZ();
       if (tokens.length > 1) {
         x = parseDouble(tokens[1]);
       }
       if (tokens.length > 2) {
         y = parseDouble(tokens[2]);
       }
       if (tokens.length > 3) {
         z = parseDouble(tokens[3]);
       }
       if (tokens.length > 4) {
         forceConstant = parseDouble(tokens[4]);
       }
       if (tokens.length > 5) {
         flatBottom = parseDouble(tokens[5]);
       }
       logger.fine(format(
           " Restrain-Position of %s to (%12.6f, %12.6f, %12.6f) with K=%8.4f and D=%8.4f",
           atom, x, y, z, forceConstant, flatBottom));
       coordinates = new double[3][1];
       coordinates[0][0] = x;
       coordinates[1][0] = y;
       coordinates[2][0] = z;
     }
     return new RestrainPosition(atomArray, coordinates, forceConstant, flatBottom, useLambda);
   }
 }