// ******************************************************************************
   //
   // 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.crystal;
  
  import static ffx.numerics.math.DoubleMath.dot;
  import static ffx.numerics.math.MatrixMath.mat3Inverse;
  import static ffx.numerics.math.MatrixMath.mat4Mat4;
  import static ffx.numerics.math.ScalarMath.mod;
  import static java.lang.Double.parseDouble;
  import static java.lang.String.format;
  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.random;
  import static org.apache.commons.math3.util.FastMath.rint;
  import static org.apache.commons.math3.util.FastMath.sin;
  import static org.apache.commons.math3.util.FastMath.sqrt;
  
  /**
   * The SymOp class defines the rotation and translation of a single symmetry operator.
   *
   * @author Michael J. Schnieders
   * @see SpaceGroup
   * @since 1.0
   */
  public class SymOp {
  
    /**
     * Constant <code>ZERO = 0.0</code>
     */
    private static final double ZERO = 0.0;
    /**
     * Constant <code>ZERO_ROTATION = {{1.0, 0.0, 0.0}, {0.0, 1.0, 0.0}, {0.0, 0.0, 1.0}}</code>
     */
    public static final double[][] ZERO_ROTATION = {
        {1.0, ZERO, ZERO},
        {ZERO, 1.0, ZERO},
        {ZERO, ZERO, 1.0}};
    /**
     * Constant <code>Tr_0_0_0={ZERO, ZERO, ZERO}</code>
     */
    public static final double[] Tr_0_0_0 = {ZERO, ZERO, ZERO};
    /**
     * Constant <code>f12 = 1.0 / 2.0</code>
     */
    private static final double f12 = 1.0 / 2.0;
    /**
     * Constant <code>Tr_12_0_12={f12, ZERO, f12}</code>
     */
    static final double[] Tr_12_0_12 = {f12, ZERO, f12};
    /**
     * Constant <code>Tr_0_12_12={ZERO, f12, f12}</code>
     */
    static final double[] Tr_0_12_12 = {ZERO, f12, f12};
    /**
     * Constant <code>Tr_12_12_0={f12, f12, ZERO}</code>
     */
    static final double[] Tr_12_12_0 = {f12, f12, ZERO};
    /**
     * Constant <code>Tr_12_12_12={f12, f12, f12}</code>
     */
    static final double[] Tr_12_12_12 = {f12, f12, f12};
    /**
     * Constant <code>Tr_0_12_0={ZERO, f12, ZERO}</code>
     */
   static final double[] Tr_0_12_0 = {ZERO, f12, ZERO};
   /**
    * Constant <code>Tr_12_0_0={f12, ZERO, ZERO}</code>
    */
   static final double[] Tr_12_0_0 = {f12, ZERO, ZERO};
   /**
    * Constant <code>Tr_0_0_12={ZERO, ZERO, f12}</code>
    */
   static final double[] Tr_0_0_12 = {ZERO, ZERO, f12};
   /**
    * Constant <code>f13 = 1.0 / 3.0</code>
    */
   private static final double f13 = 1.0 / 3.0;
   /**
    * Constant <code>Tr_0_0_13={ZERO, ZERO, f13}</code>
    */
   static final double[] Tr_0_0_13 = {ZERO, ZERO, f13};
   /**
    * Constant <code>f23 = 2.0 / 3.0</code>
    */
   private static final double f23 = 2.0 / 3.0;
   /**
    * Constant <code>Tr_23_13_13={f23, f13, f13}</code>
    */
   static final double[] Tr_23_13_13 = {f23, f13, f13};
   /**
    * Constant <code>Tr_13_23_23={f13, f23, f23}</code>
    */
   static final double[] Tr_13_23_23 = {f13, f23, f23};
   /**
    * Constant <code>Tr_0_0_23={ZERO, ZERO, f23}</code>
    */
   static final double[] Tr_0_0_23 = {ZERO, ZERO, f23};
   /**
    * Constant <code>f14 = 1.0 / 4.0</code>
    */
   private static final double f14 = 1.0 / 4.0;
   /**
    * Constant <code>Tr_12_0_14={f12, ZERO, f14}</code>
    */
   static final double[] Tr_12_0_14 = {f12, ZERO, f14};
   /**
    * Constant <code>Tr_0_12_14={ZERO, f12, f14}</code>
    */
   static final double[] Tr_0_12_14 = {ZERO, f12, f14};
   /**
    * Constant <code>Tr_14_14_14={f14, f14, f14}</code>
    */
   static final double[] Tr_14_14_14 = {f14, f14, f14};
   /**
    * Constant <code>Tr_12_12_14={f12, f12, f14}</code>
    */
   static final double[] Tr_12_12_14 = {f12, f12, f14};
   /**
    * Constant <code>Tr_0_0_14={ZERO, ZERO, f14}</code>
    */
   static final double[] Tr_0_0_14 = {ZERO, ZERO, f14};
   /**
    * Constant <code>f34 = 3.0 / 4.0</code>
    */
   private static final double f34 = 3.0 / 4.0;
   /**
    * Constant <code>Tr_0_0_34={ZERO, ZERO, f34}</code>
    */
   static final double[] Tr_0_0_34 = {ZERO, ZERO, f34};
   /**
    * Constant <code>Tr_12_0_34={f12, ZERO, f34}</code>
    */
   static final double[] Tr_12_0_34 = {f12, ZERO, f34};
   /**
    * Constant <code>Tr_0_12_34={ZERO, f12, f34}</code>
    */
   static final double[] Tr_0_12_34 = {ZERO, f12, f34};
   /**
    * Constant <code>Tr_34_14_14={f34, f14, f14}</code>
    */
   static final double[] Tr_34_14_14 = {f34, f14, f14};
   /**
    * Constant <code>Tr_14_14_34={f14, f14, f34}</code>
    */
   static final double[] Tr_14_14_34 = {f14, f14, f34};
   /**
    * Constant <code>Tr_14_34_14={f14, f34, f14}</code>
    */
   static final double[] Tr_14_34_14 = {f14, f34, f14};
   /**
    * Constant <code>Tr_12_12_34={f12, f12, f34}</code>
    */
   static final double[] Tr_12_12_34 = {f12, f12, f34};
   /**
    * Constant <code>Tr_14_34_34={f14, f34, f34}</code>
    */
   static final double[] Tr_14_34_34 = {f14, f34, f34};
   /**
    * Constant <code>Tr_34_34_14={f34, f34, f14}</code>
    */
   static final double[] Tr_34_34_14 = {f34, f34, f14};
   /**
    * Constant <code>Tr_34_34_34={f34, f34, f34}</code>
    */
   static final double[] Tr_34_34_34 = {f34, f34, f34};
   /**
    * Constant <code>Tr_34_14_34={f34, f14, f34}</code>
    */
   static final double[] Tr_34_14_34 = {f34, f14, f34};
   /**
    * Constant <code>f16 = 1.0 / 6.0</code>
    */
   private static final double f16 = 1.0 / 6.0;
   /**
    * Constant <code>Tr_13_23_16={f13, f23, f16}</code>
    */
   static final double[] Tr_13_23_16 = {f13, f23, f16};
   /**
    * Constant <code>Tr_0_0_16={ZERO, ZERO, f16}</code>
    */
   static final double[] Tr_0_0_16 = {ZERO, ZERO, f16};
   /**
    * Constant <code>f56 = 5.0 / 6.0</code>
    */
   private static final double f56 = 5.0 / 6.0;
   /**
    * Constant <code>Tr_0_0_56={ZERO, ZERO, f56}</code>
    */
   static final double[] Tr_0_0_56 = {ZERO, ZERO, f56};
   /**
    * Constant <code>Tr_23_13_56={f23, f13, f56}</code>
    */
   static final double[] Tr_23_13_56 = {f23, f13, f56};
   /**
    * Constant <code>X = {1.0, ZERO, ZERO}</code>
    */
   private static final double[] X = {1.0, ZERO, ZERO};
   /**
    * Constant <code>Y = {ZERO, 1.0, ZERO}</code>
    */
   private static final double[] Y = {ZERO, 1.0, ZERO};
   /**
    * Constant <code>Z = {ZERO, ZERO, 1.0}</code>
    */
   private static final double[] Z = {ZERO, ZERO, 1.0};
   /**
    * Constant <code>Rot_Y_Z_X={Y, Z, X}</code>
    */
   static final double[][] Rot_Y_Z_X = {Y, Z, X};
   /**
    * Constant <code>Rot_X_Y_Z={X, Y, Z}</code>
    */
   static final double[][] Rot_X_Y_Z = {X, Y, Z};
   /**
    * Constant <code>Rot_Z_X_Y={Z, X, Y}</code>
    */
   static final double[][] Rot_Z_X_Y = {Z, X, Y};
   /**
    * Constant <code>Rot_X_Z_Y={X, Z, Y}</code>
    */
   static final double[][] Rot_X_Z_Y = {X, Z, Y};
   /**
    * Constant <code>Rot_Z_Y_X={Z, Y, X}</code>
    */
   static final double[][] Rot_Z_Y_X = {Z, Y, X};
   /**
    * Constant <code>Rot_Y_X_Z={Y, X, Z}</code>
    */
   static final double[][] Rot_Y_X_Z = {Y, X, Z};
   /**
    * Constant <code>mX = {-1.0, ZERO, ZERO}</code>
    */
   private static final double[] mX = {-1.0, ZERO, ZERO};
   /**
    * Constant <code>Rot_Y_mX_Z={Y, mX, Z}</code>
    */
   static final double[][] Rot_Y_mX_Z = {Y, mX, Z};
   /**
    * Constant <code>Rot_mX_Z_Y={mX, Z, Y}</code>
    */
   static final double[][] Rot_mX_Z_Y = {mX, Z, Y};
   /**
    * Constant <code>Rot_Y_Z_mX={Y, Z, mX}</code>
    */
   static final double[][] Rot_Y_Z_mX = {Y, Z, mX};
   /**
    * Constant <code>Rot_mX_Y_Z={mX, Y, Z}</code>
    */
   static final double[][] Rot_mX_Y_Z = {mX, Y, Z};
   /**
    * Constant <code>Rot_Z_Y_mX={Z, Y, mX}</code>
    */
   static final double[][] Rot_Z_Y_mX = {Z, Y, mX};
   /**
    * Constant <code>Rot_Z_mX_Y={Z, mX, Y}</code>
    */
   static final double[][] Rot_Z_mX_Y = {Z, mX, Y};
   /**
    * Constant <code>mY = {ZERO, -1.0, ZERO}</code>
    */
   private static final double[] mY = {ZERO, -1.0, ZERO};
   /**
    * Constant <code>Rot_Z_mY_X={Z, mY, X}</code>
    */
   static final double[][] Rot_Z_mY_X = {Z, mY, X};
   /**
    * Constant <code>Rot_X_Z_mY={X, Z, mY}</code>
    */
   static final double[][] Rot_X_Z_mY = {X, Z, mY};
   /**
    * Constant <code>Rot_mY_X_Z={mY, X, Z}</code>
    */
   static final double[][] Rot_mY_X_Z = {mY, X, Z};
   /**
    * Constant <code>Rot_mY_Z_mX={mY, Z, mX}</code>
    */
   static final double[][] Rot_mY_Z_mX = {mY, Z, mX};
   /**
    * Constant <code>Rot_mY_Z_X={mY, Z, X}</code>
    */
   static final double[][] Rot_mY_Z_X = {mY, Z, X};
   /**
    * Constant <code>Rot_Z_X_mY={Z, X, mY}</code>
    */
   static final double[][] Rot_Z_X_mY = {Z, X, mY};
   /**
    * Constant <code>Rot_Z_mX_mY={Z, mX, mY}</code>
    */
   static final double[][] Rot_Z_mX_mY = {Z, mX, mY};
   /**
    * Constant <code>Rot_mX_Z_mY={mX, Z, mY}</code>
    */
   static final double[][] Rot_mX_Z_mY = {mX, Z, mY};
   /**
    * Constant <code>Rot_X_mY_Z={X, mY, Z}</code>
    */
   static final double[][] Rot_X_mY_Z = {X, mY, Z};
   /**
    * Constant <code>Rot_mY_mX_Z={mY, mX, Z}</code>
    */
   static final double[][] Rot_mY_mX_Z = {mY, mX, Z};
   /**
    * Constant <code>Rot_Z_mY_mX={Z, mY, mX}</code>
    */
   static final double[][] Rot_Z_mY_mX = {Z, mY, mX};
   /**
    * Constant <code>Rot_mX_mY_Z={mX, mY, Z}</code>
    */
   static final double[][] Rot_mX_mY_Z = {mX, mY, Z};
   /**
    * Constant <code>mZ = {ZERO, ZERO, -1.0}</code>
    */
   private static final double[] mZ = {ZERO, ZERO, -1.0};
   /**
    * Constant <code>Rot_Y_mX_mZ={Y, mX, mZ}</code>
    */
   static final double[][] Rot_Y_mX_mZ = {Y, mX, mZ};
   /**
    * Constant <code>Rot_mX_Y_mZ={mX, Y, mZ}</code>
    */
   static final double[][] Rot_mX_Y_mZ = {mX, Y, mZ};
   /**
    * Constant <code>Rot_X_mZ_Y={X, mZ, Y}</code>
    */
   static final double[][] Rot_X_mZ_Y = {X, mZ, Y};
   /**
    * Constant <code>Rot_mY_mZ_X={mY, mZ, X}</code>
    */
   static final double[][] Rot_mY_mZ_X = {mY, mZ, X};
   /**
    * Constant <code>Rot_Y_X_mZ={Y, X, mZ}</code>
    */
   static final double[][] Rot_Y_X_mZ = {Y, X, mZ};
   /**
    * Constant <code>Rot_Y_mZ_X={Y, mZ, X}</code>
    */
   static final double[][] Rot_Y_mZ_X = {Y, mZ, X};
   /**
    * Constant <code>Rot_mX_mY_mZ={mX, mY, mZ}</code>
    */
   static final double[][] Rot_mX_mY_mZ = {mX, mY, mZ};
   /**
    * Constant <code>Rot_X_Y_mZ={X, Y, mZ}</code>
    */
   static final double[][] Rot_X_Y_mZ = {X, Y, mZ};
   /**
    * Constant <code>Rot_mZ_mY_mX={mZ, mY, mX}</code>
    */
   static final double[][] Rot_mZ_mY_mX = {mZ, mY, mX};
   /**
    * Constant <code>Rot_X_mZ_mY={X, mZ, mY}</code>
    */
   static final double[][] Rot_X_mZ_mY = {X, mZ, mY};
   /**
    * Constant <code>Rot_mY_mX_mZ={mY, mX, mZ}</code>
    */
   static final double[][] Rot_mY_mX_mZ = {mY, mX, mZ};
   /**
    * Constant <code>Rot_mY_X_mZ={mY, X, mZ}</code>
    */
   static final double[][] Rot_mY_X_mZ = {mY, X, mZ};
   /**
    * Constant <code>Rot_mX_mZ_mY={mX, mZ, mY}</code>
    */
   static final double[][] Rot_mX_mZ_mY = {mX, mZ, mY};
   /**
    * Constant <code>Rot_mZ_mX_mY={mZ, mX, mY}</code>
    */
   static final double[][] Rot_mZ_mX_mY = {mZ, mX, mY};
   /**
    * Constant <code>Rot_mZ_mY_X={mZ, mY, X}</code>
    */
   static final double[][] Rot_mZ_mY_X = {mZ, mY, X};
   /**
    * Constant <code>Rot_mZ_Y_mX={mZ, Y, mX}</code>
    */
   static final double[][] Rot_mZ_Y_mX = {mZ, Y, mX};
   /**
    * Constant <code>Rot_mZ_mX_Y={mZ, mX, Y}</code>
    */
   static final double[][] Rot_mZ_mX_Y = {mZ, mX, Y};
   /**
    * Constant <code>Rot_mX_mZ_Y={mX, mZ, Y}</code>
    */
   static final double[][] Rot_mX_mZ_Y = {mX, mZ, Y};
   /**
    * Constant <code>Rot_X_mY_mZ={X, mY, mZ}</code>
    */
   static final double[][] Rot_X_mY_mZ = {X, mY, mZ};
   /**
    * Constant <code>Rot_mZ_X_Y={mZ, X, Y}</code>
    */
   static final double[][] Rot_mZ_X_Y = {mZ, X, Y};
   /**
    * Constant <code>Rot_Y_mZ_mX={Y, mZ, mX}</code>
    */
   static final double[][] Rot_Y_mZ_mX = {Y, mZ, mX};
   /**
    * Constant <code>Rot_mY_mZ_mX={mY, mZ, mX}</code>
    */
   static final double[][] Rot_mY_mZ_mX = {mY, mZ, mX};
   /**
    * Constant <code>Rot_mZ_Y_X={mZ, Y, X}</code>
    */
   static final double[][] Rot_mZ_Y_X = {mZ, Y, X};
   /**
    * Constant <code>Rot_mZ_X_mY={mZ, X, mY}</code>
    */
   static final double[][] Rot_mZ_X_mY = {mZ, X, mY};
   /**
    * Constant <code>XmY = {1.0, -1.0, ZERO}</code>
    */
   private static final double[] XmY = {1.0, -1.0, ZERO};
   /**
    * Constant <code>Rot_XmY_X_mZ={XmY, X, mZ}</code>
    */
   static final double[][] Rot_XmY_X_mZ = {XmY, X, mZ};
   /**
    * Constant <code>Rot_XmY_X_Z={XmY, X, Z}</code>
    */
   static final double[][] Rot_XmY_X_Z = {XmY, X, Z};
   /**
    * Constant <code>Rot_XmY_mY_Z={XmY, mY, Z}</code>
    */
   static final double[][] Rot_XmY_mY_Z = {XmY, mY, Z};
   /**
    * Constant <code>Rot_X_XmY_Z={X, XmY, Z}</code>
    */
   static final double[][] Rot_X_XmY_Z = {X, XmY, Z};
   /**
    * Constant <code>Rot_X_XmY_mZ={X, XmY, mZ}</code>
    */
   static final double[][] Rot_X_XmY_mZ = {X, XmY, mZ};
   /**
    * Constant <code>Rot_mY_XmY_mZ={mY, XmY, mZ}</code>
    */
   static final double[][] Rot_mY_XmY_mZ = {mY, XmY, mZ};
   /**
    * Constant <code>Rot_mY_XmY_Z={mY, XmY, Z}</code>
    */
   static final double[][] Rot_mY_XmY_Z = {mY, XmY, Z};
   /**
    * Constant <code>Rot_XmY_mY_mZ={XmY, mY, mZ}</code>
    */
   static final double[][] Rot_XmY_mY_mZ = {XmY, mY, mZ};
   /**
    * Constant <code>mXY = {-1.0, 1.0, ZERO}</code>
    */
   private static final double[] mXY = {-1.0, 1.0, ZERO};
   /**
    * Constant <code>Rot_Y_mXY_Z={Y, mXY, Z}</code>
    */
   static final double[][] Rot_Y_mXY_Z = {Y, mXY, Z};
   /**
    * Constant <code>Rot_mX_mXY_mZ={mX, mXY, mZ}</code>
    */
   static final double[][] Rot_mX_mXY_mZ = {mX, mXY, mZ};
   /**
    * Constant <code>Rot_mXY_Y_Z={mXY, Y, Z}</code>
    */
   static final double[][] Rot_mXY_Y_Z = {mXY, Y, Z};
   /**
    * Constant <code>Rot_mXY_mX_Z={mXY, mX, Z}</code>
    */
   static final double[][] Rot_mXY_mX_Z = {mXY, mX, Z};
   /**
    * Constant <code>Rot_mXY_Y_mZ={mXY, Y, mZ}</code>
    */
   static final double[][] Rot_mXY_Y_mZ = {mXY, Y, mZ};
   /**
    * Constant <code>Rot_mXY_mX_mZ={mXY, mX, mZ}</code>
    */
   static final double[][] Rot_mXY_mX_mZ = {mXY, mX, mZ};
   /**
    * Constant <code>Rot_mX_mXY_Z={mX, mXY, Z}</code>
    */
   static final double[][] Rot_mX_mXY_Z = {mX, mXY, Z};
   /**
    * Constant <code>Rot_Y_mXY_mZ={Y, mXY, mZ}</code>
    */
   static final double[][] Rot_Y_mXY_mZ = {Y, mXY, mZ};
   /**
    * The rotation matrix in fractional coordinates.
    */
   public final double[][] rot;
   /**
    * The translation vector in fractional coordinates.
    */
   public final double[] tr;
   /**
    * A mask equal to 0 for X-coordinates.
    */
   private static final int XX = 0;
   /**
    * A mask equal to 1 for Y-coordinates.
    */
   private static final int YY = 1;
   /**
    * A mask equal to 2 for Z-coordinates.
    */
   private static final int ZZ = 2;
   /**
    * Replicates position for the given symmetry operator (LxMxN).
    */
   public final int[] replicatesVector;
 
   /**
    * The SymOp constructor using a rotation matrix and translation vector.
    *
    * @param rot The rotation matrix.
    * @param tr  The translation vector.
    */
   public SymOp(double[][] rot, double[] tr) {
     this.rot = rot;
     this.tr = tr;
     replicatesVector = new int[]{0, 0, 0};
   }
 
   /**
    * The SymOp constructor using a rotation matrix and translation vector.
    *
    * @param rot              The rotation matrix.
    * @param tr               The translation vector.
    * @param replicatesVector Describes symmetry operators location within replicates crystal.
    */
   public SymOp(double[][] rot, double[] tr, int[] replicatesVector) {
     this.rot = rot;
     this.tr = tr;
     this.replicatesVector = replicatesVector;
   }
 
   /**
    * The SymOp constructor using a 4x4 matrix.
    *
    * @param m The rotation matrix and translation vector as a 4x4 matrix.
    */
   public SymOp(double[][] m) {
     this.rot = new double[3][3];
     rot[0][0] = m[0][0];
     rot[0][1] = m[0][1];
     rot[0][2] = m[0][2];
     rot[1][0] = m[1][0];
     rot[1][1] = m[1][1];
     rot[1][2] = m[1][2];
     rot[2][0] = m[2][0];
     rot[2][1] = m[2][1];
     rot[2][2] = m[2][2];
 
     this.tr = new double[3];
     tr[0] = m[0][3] / m[3][3];
     tr[1] = m[1][3] / m[3][3];
     tr[2] = m[2][3] / m[3][3];
 
     replicatesVector = new int[]{0, 0, 0};
   }
 
   /**
    * symPhaseShift
    *
    * @param hkl an array of double.
    * @return a double.
    */
   public double symPhaseShift(double[] hkl) {
     // Apply translation
     return -2.0 * PI * (hkl[0] * tr[0] + hkl[1] * tr[1] + hkl[2] * tr[2]);
   }
 
   /**
    * symPhaseShift
    *
    * @param hkl a {@link HKL} object.
    * @return a double.
    */
   public double symPhaseShift(HKL hkl) {
     // Apply translation
     return -2.0 * PI * (hkl.getH() * tr[0] + hkl.getK() * tr[1] + hkl.getL() * tr[2]);
   }
 
   /**
    * Return the SymOp as a 4x4 matrix.
    *
    * @return A 4x4 matrix representation of the SymOp.
    */
   public double[][] asMatrix() {
     return new double[][]{
         {rot[0][0], rot[0][1], rot[0][2], tr[0]},
         {rot[1][0], rot[1][1], rot[1][2], tr[1]},
         {rot[2][0], rot[2][1], rot[2][2], tr[2]},
         {0.0, 0.0, 0.0, 1.0}};
   }
 
   /**
    * Return the combined SymOp that is equivalent to first applying <code>this</code> SymOp and then
    * the argument. Note: Applied as rotation then translation.
    * <code>X' = S_arg(S_this(X))</code>
    * <code>X' = S_combined(X)</code>
    *
    * @param symOp The SymOp to append to <code>this</code> SymOp.
    * @return The combined SymOp.
    */
   public SymOp append(SymOp symOp) {
     return new SymOp(mat4Mat4(symOp.asMatrix(), asMatrix()));
   }
 
   /**
    * Return the combined SymOp that is equivalent to first applying the argument and then
    * <code>this</code> SymOp. Note: Applied as rotation then translation.
    * <code>X' = S_this(S_arg(X))</code>
    * <code>X' = S_combined(X)</code>
    *
    * @param symOp The SymOp to prepend to <code>this</code> SymOp.
    * @return The combined SymOp.
    */
   public SymOp prepend(SymOp symOp) {
     return new SymOp(mat4Mat4(asMatrix(), symOp.asMatrix()));
   }
 
   /**
    * Return the combined SymOp that is equivalent to first applying symOp1 and then SymOp2. Note:
    * Applied as rotation then translation.
    * <p>
    * <code>X' = S_2(S_1(X))</code>
    * <code>X' = S_combined(X)</code>
    *
    * @param symOp1 The fist SymOp.
    * @param symOp2 The second SymOp.
    * @return The combined SymOp.
    */
   public static SymOp combineSymOps(SymOp symOp1, SymOp symOp2) {
     return new SymOp(mat4Mat4(symOp2.asMatrix(), symOp1.asMatrix()));
   }
 
   /**
    * Apply a Cartesian symmetry operator to an array of Cartesian coordinates. If the arrays x, y or
    * z are null or not of length n, the method returns immediately. If mateX, mateY or mateZ are null
    * or not of length n, the method returns immediately.
    *
    * @param n     Number of atoms.
    * @param x     Input cartesian x-coordinates.
    * @param y     Input cartesian y-coordinates.
    * @param z     Input cartesian z-coordinates.
    * @param mateX Output cartesian x-coordinates.
    * @param mateY Output cartesian y-coordinates.
    * @param mateZ Output cartesian z-coordinates.
    * @param symOp The cartesian symmetry operator.
    */
   public static void applyCartSymOp(int n, double[] x, double[] y, double[] z,
                                     double[] mateX, double[] mateY, double[] mateZ, SymOp symOp) {
     if (x == null || y == null || z == null) {
       throw new IllegalArgumentException("The input arrays x, y and z must not be null.");
     }
     if (x.length < n || y.length < n || z.length < n) {
       throw new IllegalArgumentException("The input arrays x, y and z must be of length n: " + n);
     }
     if (mateX == null || mateY == null || mateZ == null) {
       throw new IllegalArgumentException("The output arrays mateX, mateY and mateZ must not be null.");
     }
     if (mateX.length < n || mateY.length < n || mateZ.length < n) {
       throw new IllegalArgumentException("The output arrays mateX, mateY and mateZ must be of length n: " + n);
     }
 
     final double[][] rot = symOp.rot;
     final double[] trans = symOp.tr;
 
     final double rot00 = rot[0][0];
     final double rot10 = rot[1][0];
     final double rot20 = rot[2][0];
     final double rot01 = rot[0][1];
     final double rot11 = rot[1][1];
     final double rot21 = rot[2][1];
     final double rot02 = rot[0][2];
     final double rot12 = rot[1][2];
     final double rot22 = rot[2][2];
     final double t0 = trans[0];
     final double t1 = trans[1];
     final double t2 = trans[2];
     for (int i = 0; i < n; i++) {
       double xc = x[i];
       double yc = y[i];
       double zc = z[i];
       // Apply Symmetry Operator.
       mateX[i] = rot00 * xc + rot01 * yc + rot02 * zc + t0;
       mateY[i] = rot10 * xc + rot11 * yc + rot12 * zc + t1;
       mateZ[i] = rot20 * xc + rot21 * yc + rot22 * zc + t2;
     }
   }
 
   /**
    * Apply a cartesian symmetry operator to an array of coordinates.
    *
    * @param xyz   Input  cartesian coordinates.
    * @param mate  Symmetry mate  cartesian coordinates.
    * @param symOp The cartesian symmetry operator.
    */
   public static void applyCartesianSymOp(double[] xyz, double[] mate, SymOp symOp) {
     applyCartesianSymOp(xyz, mate, symOp, null);
   }
 
   /**
    * Apply a cartesian symmetry operator to an array of coordinates.
    *
    * @param xyz   Input  cartesian coordinates.
    * @param mate  Symmetry mate  cartesian coordinates.
    * @param symOp The cartesian symmetry operator.
    * @param mask  Only apply the SymOp if the per atom mask is true.
    */
   public static void applyCartesianSymOp(double[] xyz, double[] mate, SymOp symOp, boolean[] mask) {
     var rot = symOp.rot;
     var trans = symOp.tr;
 
     assert (xyz.length % 3 == 0);
     assert (xyz.length == mate.length);
     int len = xyz.length / 3;
 
     // Load the SymOp into local variables.
     var rot00 = rot[0][0];
     var rot10 = rot[1][0];
     var rot20 = rot[2][0];
     var rot01 = rot[0][1];
     var rot11 = rot[1][1];
     var rot21 = rot[2][1];
     var rot02 = rot[0][2];
     var rot12 = rot[1][2];
     var rot22 = rot[2][2];
     var tx = trans[0];
     var ty = trans[1];
     var tz = trans[2];
 
     if (mask == null) {
       for (int i = 0; i < len; i++) {
         int index = i * 3;
         var xc = xyz[index + XX];
         var yc = xyz[index + YY];
         var zc = xyz[index + ZZ];
         // Apply Symmetry Operator.
         mate[index + XX] = rot00 * xc + rot01 * yc + rot02 * zc + tx;
         mate[index + YY] = rot10 * xc + rot11 * yc + rot12 * zc + ty;
         mate[index + ZZ] = rot20 * xc + rot21 * yc + rot22 * zc + tz;
       }
     } else {
       for (int i = 0; i < len; i++) {
         int index = i * 3;
         var xc = xyz[index + XX];
         var yc = xyz[index + YY];
         var zc = xyz[index + ZZ];
         if (mask[i]) {
           // Apply Symmetry Operator.
           mate[index + XX] = rot00 * xc + rot01 * yc + rot02 * zc + tx;
           mate[index + YY] = rot10 * xc + rot11 * yc + rot12 * zc + ty;
           mate[index + ZZ] = rot20 * xc + rot21 * yc + rot22 * zc + tz;
         } else {
           mate[index + XX] = xc;
           mate[index + YY] = yc;
           mate[index + ZZ] = zc;
         }
       }
     }
   }
 
   /**
    * Apply a fractional symmetry operator to one set of coordinates.
    *
    * @param xyz   Input fractional coordinates.
    * @param mate  Symmetry mate fractional coordinates.
    * @param symOp The fractional symmetry operator.
    */
   public static void applyFracSymOp(double[] xyz, double[] mate, SymOp symOp) {
     var rot = symOp.rot;
     var trans = symOp.tr;
     var xf = xyz[0];
     var yf = xyz[1];
     var zf = xyz[2];
     // Apply Symmetry Operator.
     mate[0] = rot[0][0] * xf + rot[0][1] * yf + rot[0][2] * zf + trans[0];
     mate[1] = rot[1][0] * xf + rot[1][1] * yf + rot[1][2] * zf + trans[1];
     mate[2] = rot[2][0] * xf + rot[2][1] * yf + rot[2][2] * zf + trans[2];
   }
 
   /**
    * Apply a symmetry operator to one set of coordinates.
    *
    * @param h     Input coordinates.
    * @param k     Input coordinates.
    * @param l     Input coordinates.
    * @param mate  Symmetry mate coordinates.
    * @param symOp The symmetry operator.
    * @param nx    number of unit cell translations
    * @param ny    number of unit cell translations
    * @param nz    number of unit cell translations
    */
   public static void applySymOp(int h, int k, int l, int[] mate, SymOp symOp, int nx, int ny, int nz) {
     var rot = symOp.rot;
     var trans = symOp.tr;
     // Apply Symmetry Operator.
     mate[0] =
         (int) rot[0][0] * h + (int) rot[0][1] * k + (int) rot[0][2] * l + (int) rint(nx * trans[0]);
     mate[1] =
         (int) rot[1][0] * h + (int) rot[1][1] * k + (int) rot[1][2] * l + (int) rint(ny * trans[1]);
     mate[2] =
         (int) rot[2][0] * h + (int) rot[2][1] * k + (int) rot[2][2] * l + (int) rint(nz * trans[2]);
     mate[0] = mod(mate[0], nx);
     mate[1] = mod(mate[1], ny);
     mate[2] = mod(mate[2], nz);
   }
 
   /**
    * Apply a symmetry operator to one HKL.
    *
    * @param hkl   Input HKL.
    * @param mate  Symmetry mate HKL.
    * @param symOp The symmetry operator.
    */
   public static void applySymRot(HKL hkl, HKL mate, SymOp symOp) {
     var rot = symOp.rot;
     double h = hkl.getH();
     double k = hkl.getK();
     double l = hkl.getL();
     double hs = rot[0][0] * h + rot[0][1] * k + rot[0][2] * l;
     double ks = rot[1][0] * h + rot[1][1] * k + rot[1][2] * l;
     double ls = rot[2][0] * h + rot[2][1] * k + rot[2][2] * l;
     // Convert back to HKL
     mate.setH((int) rint(hs));
     mate.setK((int) rint(ks));
     mate.setL((int) rint(ls));
   }
 
   /**
    * Apply a Cartesian symmetry rotation to an array of Cartesian coordinates. The length of xyz must
    * be divisible by 3 and mate must have the same length.
    *
    * @param xyz   Input cartesian x, y, z-coordinates.
    * @param mate  Output cartesian x, y, z-coordinates.
    * @param symOp The fractional symmetry operator.
    */
   public static void applyCartesianSymRot(double[] xyz, double[] mate, SymOp symOp) {
     applyCartesianSymRot(xyz, mate, symOp, null);
   }
 
   /**
    * Apply a Cartesian symmetry rotation to an array of Cartesian coordinates. The length of xyz must
    * be divisible by 3 and mate must have the same length.
    *
    * @param xyz   Input cartesian x, y, z-coordinates.
    * @param mate  Output cartesian x, y, z-coordinates.
    * @param symOp The fractional symmetry operator.
    * @param mask  Only apply the SymOp if the per atom mask is true.
    */
   public static void applyCartesianSymRot(double[] xyz, double[] mate, SymOp symOp, boolean[] mask) {
     int l = xyz.length;
     int n = l / 3;
     assert (l % 3 == 0);
     assert (mate.length == l);
 
     // Load the rotation matrix
     var rot = symOp.rot;
     var rot00 = rot[0][0];
     var rot10 = rot[1][0];
     var rot20 = rot[2][0];
     var rot01 = rot[0][1];
     var rot11 = rot[1][1];
     var rot21 = rot[2][1];
     var rot02 = rot[0][2];
     var rot12 = rot[1][2];
     var rot22 = rot[2][2];
 
     if (mask == null) {
       for (int i = 0; i < n; i++) {
         int index = i * 3;
         var xi = xyz[index + XX];
         var yi = xyz[index + YY];
         var zi = xyz[index + ZZ];
         // Apply Symmetry Operator.
         mate[index + XX] = rot00 * xi + rot01 * yi + rot02 * zi;
         mate[index + YY] = rot10 * xi + rot11 * yi + rot12 * zi;
         mate[index + ZZ] = rot20 * xi + rot21 * yi + rot22 * zi;
       }
     } else {
       for (int i = 0; i < n; i++) {
         int index = i * 3;
         var xi = xyz[index + XX];
         var yi = xyz[index + YY];
         var zi = xyz[index + ZZ];
         if (mask[i]) {
           // Apply Symmetry Operator.
           mate[index + XX] = rot00 * xi + rot01 * yi + rot02 * zi;
           mate[index + YY] = rot10 * xi + rot11 * yi + rot12 * zi;
           mate[index + ZZ] = rot20 * xi + rot21 * yi + rot22 * zi;
         } else {
           mate[index + XX] = xi;
           mate[index + YY] = yi;
           mate[index + ZZ] = zi;
         }
       }
     }
   }
 
   /**
    * Apply a transpose rotation symmetry operator to one HKL.
    *
    * @param hkl   Input HKL.
    * @param mate  Symmetry mate HKL.
    * @param symOp The symmetry operator.
    */
   public static void applyTransSymRot(HKL hkl, HKL mate, SymOp symOp) {
     double[][] rot = symOp.rot;
     double h = hkl.getH();
     double k = hkl.getK();
     double l = hkl.getL();
     // Apply transpose Symmetry Operator.
     double hs = rot[0][0] * h + rot[1][0] * k + rot[2][0] * l;
     double ks = rot[0][1] * h + rot[1][1] * k + rot[2][1] * l;
     double ls = rot[0][2] * h + rot[1][2] * k + rot[2][2] * l;
     // Convert back to HKL
     mate.setH((int) rint(hs));
     mate.setK((int) rint(ks));
     mate.setL((int) rint(ls));
   }
 
   /**
    * Print a Sym Op matrix as a continued line string.
    *
    * @param symOp Symmetry operation to print.
    * @return Continued line string.
    */
   public static String asMatrixString(SymOp symOp) {
     double[][] values = symOp.asMatrix();
     return format("""
              %14.8f %14.8f %14.8f \\
                        %14.8f %14.8f %14.8f \\
                        %14.8f %14.8f %14.8f \\
                        %14.8f %14.8f %14.8f \
             """, values[0][0],
         values[0][1], values[0][2], values[1][0], values[1][1], values[1][2], values[2][0],
         values[2][1], values[2][2], values[0][3], values[1][3], values[2][3]);
   }
 
   /**
    * Invert a symmetry operator.
    *
    * @param symOp Original symmetry operator of which the inverse is desired.
    * @return SymOp The inverse symmetry operator of the one supplied.
    */
   public static SymOp invertSymOp(SymOp symOp) {
     var tr = symOp.tr;
     var rot = symOp.rot;
     var inv = mat3Inverse(rot);
     return new SymOp(inv,
         new double[]{-dot(inv[0], tr), -dot(inv[1], tr), -dot(inv[2], tr)});
   }
 
   /**
    * Create a SymOp from an input String.
    *
    * @param s Input <code>String</code> containing 12 white-space delimited double values.
    * @return The SymOp.
    */
   public static SymOp parse(String s) {
     String[] tokens = s.split(" +");
     if (tokens.length < 12) {
       return null;
     }
     return new SymOp(new double[][]{
         {parseDouble(tokens[0]), parseDouble(tokens[1]), parseDouble(tokens[2])},
         {parseDouble(tokens[3]), parseDouble(tokens[4]), parseDouble(tokens[5])},
         {parseDouble(tokens[6]), parseDouble(tokens[7]), parseDouble(tokens[8])}},
         new double[]{parseDouble(tokens[9]), parseDouble(tokens[10]), parseDouble(tokens[11])});
   }
 
   /**
    * Generate a random Cartesian Symmetry Operator.
    *
    * @param scalar The range of translations will be from -scalar/2 .. scalar/2.
    * @return A Cartesian SymOp with a random rotation and translation.
    */
   public static SymOp randomSymOpFactory(double scalar) {
     double[] tr = {scalar * (random() - 0.5), scalar * (random() - 0.5), scalar * (random() - 0.5)};
     return randomSymOpFactory(tr);
   }
 
   /**
    * Generate a random Cartesian Symmetry Operator.
    *
    * <p>The random rotation matrix is derived from: Arvo, James (1992), "Fast random rotation
    * matrices", in David Kirk, Graphics Gems III, San Diego: Academic Press Professional, pp.
    * 117–120, ISBN 978-0-12-409671-4
    *
    * @param tr The translations to apply.
    * @return A Cartesian SymOp with a random rotation and translation.
    */
   public static SymOp randomSymOpFactory(double[] tr) {
     double[][] rot = new double[3][3];
     double PI2 = 2.0 * PI;
     double[] x = new double[3];
     x[0] = random();
     x[1] = random();
     x[2] = random();
     /* Rotation about the pole (Z).      */
     double theta = x[0] * PI2;
     /* For direction of pole deflection. */
     double phi = x[1] * PI2;
     /* For magnitude of pole deflection. */
     double z = x[2] * 2.0;
     /*
      Compute a vector V used for distributing points over the sphere via
      the reflection I - V Transpose(V). This formulation of V will
      guarantee that if x[1] and x[2] are uniformly distributed, the
      reflected points will be uniform on the sphere. Note that V has
      length sqrt(2) to eliminate the 2 in the Householder matrix.
     */
     double r = sqrt(z);
     double Vx = sin(phi) * r;
     double Vy = cos(phi) * r;
     double Vz = sqrt(2.0 - z);
     /*
      Compute the row vector S = Transpose(V) * R, where R is a simple
      rotation by theta about the z-axis. No need to compute Sz since it's
      just Vz.
     */
     double st = sin(theta);
     double ct = cos(theta);
     double Sx = Vx * ct - Vy * st;
     double Sy = Vx * st + Vy * ct;
 
     // Construct the rotation matrix ( V Transpose(V) - I ) R, which is equivalent to V S - R.
     rot[0][0] = Vx * Sx - ct;
     rot[0][1] = Vx * Sy - st;
     rot[0][2] = Vx * Vz;
     rot[1][0] = Vy * Sx + st;
     rot[1][1] = Vy * Sy - ct;
     rot[1][2] = Vy * Vz;
     rot[2][0] = Vz * Sx;
     rot[2][1] = Vz * Sy;
     // This equals Vz * Vz - 1.0
     rot[2][2] = 1.0 - z;
 
     return new SymOp(rot, tr);
   }
 
   /**
    * trtoString
    *
    * @param tr a double.
    * @return a {@link java.lang.String} object.
    */
   private static String trtoString(double tr) {
     if (tr == f12) {
       return "+1/2";
     }
     if (tr == f13) {
       return "+1/3";
     }
     if (tr == f23) {
       return "+2/3";
     }
     if (tr == f14) {
       return "+1/4";
     }
     if (tr == f34) {
       return "+3/4";
     }
     if (tr == f16) {
       return "+1/6";
     }
     if (tr == f56) {
       return "+5/6";
     }
 
     return "";
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public String toString() {
     StringBuilder sb = new StringBuilder(" Rotation operator:\n");
     sb.append(format(" [[%4.1f,%4.1f,%4.1f]\n  [%4.1f,%4.1f,%4.1f]\n  [%4.1f,%4.1f,%4.1f]]\n",
         rot[0][0], rot[0][1], rot[0][2],
         rot[1][0], rot[1][1], rot[1][2],
         rot[2][0], rot[2][1], rot[2][2]));
     sb.append(" Translation:\n");
     sb.append(format(" [%4.2f,%4.2f,%4.2f]", tr[0], tr[1], tr[2]));
     return sb.toString();
   }
 
   /**
    * Print the symmetry operator with double precision.
    *
    * @return String of rotation/translation with double precision.
    */
   public String toStringPrecise() {
     StringBuilder sb = new StringBuilder(" Rotation operator:\n");
     sb.append(format(
         " [[%18.16e,%18.16e,%18.16e]\n  [%18.16e,%18.16e,%18.16e]\n  [%18.16e,%18.16e,%18.16e]]\n",
         rot[0][0], rot[0][1], rot[0][2],
         rot[1][0], rot[1][1], rot[1][2],
         rot[2][0], rot[2][1], rot[2][2]));
     sb.append(" Translation:\n");
     sb.append(format(" [%18.16e,%18.16e,%18.16e]", tr[0], tr[1], tr[2]));
     return sb.toString();
   }
 
   /**
    * toXYZString
    *
    * @return a {@link java.lang.String} object.
    */
   public String toXYZString() {
     StringBuilder sb = new StringBuilder();
     for (int i = 0; i < 3; i++) {
       boolean s = false;
       if (rot[i][0] < 0.0) {
         sb.append("-X");
         s = true;
       } else if (rot[i][0] > 0.0) {
         sb.append("X");
         s = true;
       }
       if (rot[i][1] < 0.0) {
         sb.append("-Y");
         s = true;
       } else if (rot[i][1] > 0.0) {
         sb.append(s ? "+Y" : "Y");
         s = true;
       }
       if (rot[i][2] < 0.0) {
         sb.append("-Z");
       } else if (rot[i][2] > 0.0) {
         sb.append(s ? "+Z" : "Z");
       }
 
       if (tr[i] > 0.0) {
         sb.append(trtoString(tr[i]));
       }
 
       if (i < 2) {
         sb.append(", ");
       }
     }
     return sb.toString();
   }
 }