// ******************************************************************************
   //
   // 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
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  // module which is not derived from or based on this library. If you modify this
  // library, you may extend this exception to your version of the library, but
  // you are not obligated to do so. If you do not wish to do so, delete this
  // exception statement from your version.
  //
  // ******************************************************************************
  package ffx.potential.bonded;
  
  import ffx.numerics.atomic.AtomicDoubleArray3D;
  import ffx.numerics.math.DoubleMath;
  import ffx.potential.parameters.AtomType;
  import ffx.potential.parameters.ForceField;
  import ffx.potential.parameters.TorsionType;
  
  import java.io.Serial;
  import java.util.ArrayList;
  import java.util.List;
  import java.util.function.DoubleUnaryOperator;
  import java.util.logging.Logger;
  
  import static ffx.numerics.math.DoubleMath.dihedralAngle;
  import static java.lang.String.format;
  import static org.apache.commons.math3.util.FastMath.acos;
  import static org.apache.commons.math3.util.FastMath.max;
  import static org.apache.commons.math3.util.FastMath.sqrt;
  import static org.apache.commons.math3.util.FastMath.toDegrees;
  
  /**
   * The Torsion class represents a torsional angle formed between four bonded atoms.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class Torsion extends BondedTerm implements LambdaInterface {
  
    @Serial
    private static final long serialVersionUID = 1L;
  
    private static final Logger logger = Logger.getLogger(Torsion.class.getName());
    /**
     * The force field Torsion type in use.
     */
    public TorsionType torsionType = null;
    /**
     * Scale up the torsional energy by this factor.
     */
    private double torsionScale = 1.0;
    /**
     * Value of lambda.
     */
    private double lambda = 1.0;
    /**
     * Value of dE/dL.
     */
    private double dEdL = 0.0;
    /**
     * Flag to indicate lambda dependence.
     */
    private boolean lambdaTerm = false;
    /**
     * Maps global lambda to either itself or 1 - global lambda.
     */
    private final DoubleUnaryOperator lambdaMapper;
    /**
     * Set the tolerance for minimum distance and angle values.
     */
    private static final double TORSION_TOLERANCE = 1.0e-4;
  
   /**
    * Create a Torsion from 3 connected bonds (no error checking)
    *
    * @param b1 The first Bond.
    * @param b2 The middle Bond.
    * @param b3 The last Bond.
    */
   public Torsion(Bond b1, Bond b2, Bond b3) {
     super();
     bonds = new Bond[3];
     bonds[0] = b1;
     bonds[1] = b2;
     bonds[2] = b3;
     lambdaMapper = (double d) -> d;
     initialize();
   }
 
   /**
    * Log that no TorsionType exists.
    *
    * @param a0 Atom 0.
    * @param a1 Atom 1.
    * @param a2 Atom 2.
    * @param a3 Atom 3.
    */
   public static void logNoTorsionType(Atom a0, Atom a1, Atom a2, Atom a3, ForceField forceField) {
     AtomType atomType0 = a0.getAtomType();
     AtomType atomType1 = a1.getAtomType();
     AtomType atomType2 = a2.getAtomType();
     AtomType atomType3 = a3.getAtomType();
     int[] c = {atomType0.atomClass, atomType1.atomClass, atomType2.atomClass, atomType3.atomClass};
     String key = TorsionType.sortKey(c);
     StringBuilder sb = new StringBuilder(
         format("No TorsionType for key: %s\n %s -> %s\n %s -> %s\n %s -> %s\n %s -> %s", key, a0,
             atomType0, a1, atomType1, a2, atomType2, a3, atomType3));
     if (matchTorsions(a0, a1, a2, a3, forceField, sb, true) <= 0) {
       matchTorsions(a0, a1, a2, a3, forceField, sb, false);
     }
     logger.severe(sb.toString());
   }
 
   private static int matchTorsions(Atom a0, Atom a1, Atom a2, Atom a3, ForceField forceField,
                                    StringBuilder sb, boolean strict) {
     AtomType atomType0 = a0.getAtomType();
     AtomType atomType1 = a1.getAtomType();
     AtomType atomType2 = a2.getAtomType();
     AtomType atomType3 = a3.getAtomType();
     int c0 = atomType0.atomClass;
     int c1 = atomType1.atomClass;
     int c2 = atomType2.atomClass;
     int c3 = atomType3.atomClass;
     List<AtomType> types0 = forceField.getSimilarAtomTypes(atomType0);
     List<AtomType> types1 = forceField.getSimilarAtomTypes(atomType1);
     List<AtomType> types2 = forceField.getSimilarAtomTypes(atomType2);
     List<AtomType> types3 = forceField.getSimilarAtomTypes(atomType3);
     List<TorsionType> torsionTypes = new ArrayList<>();
     boolean match = false;
     for (AtomType type1 : types1) {
       for (AtomType type2 : types2) {
         // Match both inner atom classes.
         if ((type1.atomClass == c1 && type2.atomClass == c2) || (type1.atomClass == c2 && type2.atomClass == c1)) {
           for (AtomType type0 : types0) {
             for (AtomType type3 : types3) {
               // Match one distal atom class.
               if (strict) {
                 if ((type0.atomClass != c0) && (type0.atomClass != c3) && (type3.atomClass != c0) && (type3.atomClass != c3)) {
                   continue;
                 }
               }
               TorsionType torsionType = forceField.getTorsionType(type0, type1, type2, type3);
               if (torsionType != null && !torsionTypes.contains(torsionType)) {
                 if (!match) {
                   match = true;
                   sb.append("\n Similar Torsion Types:");
                 }
                 torsionTypes.add(torsionType);
                 sb.append(format("\n  %s", torsionType));
               }
             }
           }
         }
       }
     }
     return torsionTypes.size();
   }
 
   /**
    * Attempt to create a new Torsion based on the supplied bonds. There is no error checking to
    * enforce that the bonds make up a linear series of 4 bonded atoms.
    *
    * @param bond1      the first Bond.
    * @param middleBond the middle Bond.
    * @param bond3      the last Bond.
    * @param forceField the ForceField parameters to apply.
    * @return a new Torsion, or null.
    */
   static Torsion torsionFactory(Bond bond1, Bond middleBond, Bond bond3, ForceField forceField) {
     Atom a0 = bond1.getOtherAtom(middleBond);
     Atom a1 = middleBond.getAtom(0);
     Atom a2 = middleBond.getAtom(1);
     Atom a3 = bond3.getOtherAtom(middleBond);
 
     TorsionType torsionType = forceField.getTorsionType(a0.getAtomType(), a1.getAtomType(),
         a2.getAtomType(), a3.getAtomType());
 
     // No torsion type found.
     if (torsionType == null) {
       logNoTorsionType(a0, a1, a2, a3, forceField);
       return null;
     }
 
     Torsion torsion = new Torsion(bond1, middleBond, bond3);
     torsion.setTorsionType(torsionType);
     // Scale-up torsions that do not include hydrogen or halogen atoms.
     if (forceField.hasProperty("torsion-scale")) {
       // Check the identity of the terminal atoms.
       boolean isTerminal = (a0.isHydrogen() || a0.isHalogen() || a3.isHydrogen() || a3.isHalogen());
       if (!isTerminal) {
         double scale = forceField.getDouble("torsion-scale", 1.0);
         torsion.setTorsionScale(scale);
       }
     }
 
     return torsion;
   }
 
   /**
    * Set the torsion type.
    *
    * @param torsionType The TorsionType.
    */
   public void setTorsionType(TorsionType torsionType) {
     this.torsionType = torsionType;
   }
 
   /**
    * Set the torsion scale up factor.
    *
    * @param torsionScale The torsion scale up factor.
    */
   public void setTorsionScale(double torsionScale) {
     this.torsionScale = torsionScale;
   }
 
   /**
    * Get the torsion scale up factor.
    *
    * @return The torsion scale up factor.
    */
   public double getTorsionScale() {
     return torsionScale;
   }
 
   /**
    * compare
    *
    * @param a0 a {@link ffx.potential.bonded.Atom} object.
    * @param a1 a {@link ffx.potential.bonded.Atom} object.
    * @param a2 a {@link ffx.potential.bonded.Atom} object.
    * @param a3 a {@link ffx.potential.bonded.Atom} object.
    * @return a boolean.
    */
   public boolean compare(Atom a0, Atom a1, Atom a2, Atom a3) {
     if (a0 == atoms[0] && a1 == atoms[1] && a2 == atoms[2] && a3 == atoms[3]) {
       return true;
     }
     return (a0 == atoms[3] && a1 == atoms[2] && a2 == atoms[1] && a3 == atoms[0]);
   }
 
   /**
    * Compute the torsional angle in degrees.
    *
    * @return The torsion in degrees.
    */
   public double measure() {
     double angle = DoubleMath.dihedralAngle(atoms[0].getXYZ(null), atoms[1].getXYZ(null),
         atoms[2].getXYZ(null), atoms[3].getXYZ(null));
     return toDegrees(angle);
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Evaluate the Torsional Angle energy.
    */
   @Override
   public double energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad) {
     energy = 0.0;
     value = 0.0;
     dEdL = 0.0;
     // Only compute this term if at least one atom is being used.
     if (!getUse()) {
       return energy;
     }
     var atomA = atoms[0];
     var atomB = atoms[1];
     var atomC = atoms[2];
     var atomD = atoms[3];
     // Compute the value of the torsional angle.
     var va = atomA.getXYZ();
     var vb = atomB.getXYZ();
     var vc = atomC.getXYZ();
     var vd = atomD.getXYZ();
     var vba = vb.sub(va);
     var vcb = vc.sub(vb);
     var vdc = vd.sub(vc);
     var vt = vba.X(vcb);
     var vu = vcb.X(vdc);
     var rt2 = max(vt.length2(), TORSION_TOLERANCE);
     var ru2 = max(vu.length2(), TORSION_TOLERANCE);
     var rtru2 = rt2 * ru2;
     var rr = sqrt(rtru2);
     var rcb = max(vcb.length(), TORSION_TOLERANCE);
     var cosine = vt.dot(vu) / rr;
     var sine = vcb.dot(vt.X(vu)) / (rcb * rr);
     value = toDegrees(acos(cosine));
     if (sine < 0.0) {
       value = -value;
     }
 
     // Calculate the torsional energy for this angle.
     var amp = torsionType.amplitude;
     var tsin = torsionType.sine;
     var tcos = torsionType.cosine;
 
     // Add the energy for the first term.
     energy = amp[0] * (1.0 + cosine * tcos[0] + sine * tsin[0]);
     var dedphi = amp[0] * (cosine * tsin[0] - sine * tcos[0]);
     var cosprev = cosine;
     var sinprev = sine;
     var n = torsionType.terms;
 
     // Add the energy for the remaining terms.
     for (int i = 1; i < n; i++) {
       var cosn = cosine * cosprev - sine * sinprev;
       var sinn = sine * cosprev + cosine * sinprev;
       var phi = 1.0 + cosn * tcos[i] + sinn * tsin[i];
       var dphi = (1.0 + i) * (cosn * tsin[i] - sinn * tcos[i]);
       energy = energy + amp[i] * phi;
       dedphi = dedphi + amp[i] * dphi;
       cosprev = cosn;
       sinprev = sinn;
     }
 
     dEdL = torsionScale * torsionType.torsionUnit * energy;
     energy = dEdL * lambda;
 
     // Compute the torsional gradient for this angle.
     if (gradient || lambdaTerm) {
       // Chain rule terms for first derivative components.
       dedphi = torsionScale * torsionType.torsionUnit * dedphi;
       var vca = vc.sub(va);
       var vdb = vd.sub(vb);
       var dedt = vt.X(vcb).scaleI(dedphi / (rt2 * rcb));
       var dedu = vu.X(vcb).scaleI(-dedphi / (ru2 * rcb));
 
       // Compute first derivative components for this angle.
       var ga = dedt.X(vcb);
       var gb = vca.X(dedt).addI(dedu.X(vdc));
       var gc = dedt.X(vba).addI(vdb.X(dedu));
       var gd = dedu.X(vcb);
       int ia = atomA.getIndex() - 1;
       int ib = atomB.getIndex() - 1;
       int ic = atomC.getIndex() - 1;
       int id = atomD.getIndex() - 1;
       if (lambdaTerm) {
         lambdaGrad.add(threadID, ia, ga);
         lambdaGrad.add(threadID, ib, gb);
         lambdaGrad.add(threadID, ic, gc);
         lambdaGrad.add(threadID, id, gd);
       }
       if (gradient) {
         grad.add(threadID, ia, ga.scaleI(lambda));
         grad.add(threadID, ib, gb.scaleI(lambda));
         grad.add(threadID, ic, gc.scaleI(lambda));
         grad.add(threadID, id, gd.scaleI(lambda));
       }
     }
 
     return energy;
   }
 
   /**
    * If the specified atom is not a central atom of <b>this</b> torsion, the atom at the opposite end
    * is returned. These atoms are said to be 1-4 to each other.
    *
    * @param a Atom
    * @return Atom
    */
   public Atom get1_4(Atom a) {
     if (a == atoms[0]) {
       return atoms[3];
     }
     if (a == atoms[3]) {
       return atoms[0];
     }
     return null;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double getLambda() {
     return lambda;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void setLambda(double lambda) {
     if (applyAllLambda()) {
       lambdaTerm = true;
     }
     this.lambda = lambdaTerm ? lambdaMapper.applyAsDouble(lambda) : 1.0;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double getd2EdL2() {
     return 0.0;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public double getdEdL() {
     if (lambdaTerm) {
       return dEdL;
     } else {
       return 0.0;
     }
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void getdEdXdL(double[] gradient) {
     // The chain rule term is zero.
   }
 
   /**
    * Log details for this Torsional Angle energy term.
    */
   public void log() {
     logger.info(format(" %-8s %6d-%s %6d-%s %6d-%s %6d-%s %10.4f %10.4f %10.4f", "Torsional-Angle",
         atoms[0].getIndex(), atoms[0].getAtomType().name, atoms[1].getIndex(),
         atoms[1].getAtomType().name, atoms[2].getIndex(), atoms[2].getAtomType().name,
         atoms[3].getIndex(), atoms[3].getAtomType().name, value, energy, torsionScale));
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Overridden toString Method returns the Term's id.
    */
   @Override
   public String toString() {
     return format("%s  (%7.1f,%7.2f,%7.2f)", id, value, energy, torsionScale);
   }
 
   /**
    * Initialization
    */
   private void initialize() {
     atoms = new Atom[4];
     atoms[1] = bonds[0].getCommonAtom(bonds[1]);
     atoms[0] = bonds[0].get1_2(atoms[1]);
     atoms[2] = bonds[1].get1_2(atoms[1]);
     atoms[3] = bonds[2].get1_2(atoms[2]);
     atoms[0].setTorsion(this);
     atoms[1].setTorsion(this);
     atoms[2].setTorsion(this);
     atoms[3].setTorsion(this);
     setID_Key(false);
     value = dihedralAngle(atoms[0].getXYZ(null), atoms[1].getXYZ(null), atoms[2].getXYZ(null),
         atoms[3].getXYZ(null));
   }
 }