// ******************************************************************************
   //
   // 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.algorithms.dynamics.integrators;
  
  import ffx.crystal.Crystal;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.bonded.Atom;
  
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  import static java.lang.Math.abs;
  
  /**
   * The Rattle classes implements the RATTLE distance constraint method.
   *
   * @author Jill J. Hauer
   */
  public class Rattle {
  
    /**
     * Literature reference (from Tinker):
     *
     * <p>H. C. Andersen, "RATTLE: A Velocity Version of the SHAKE Algorithm for Molecular Dynamics
     * Calculations", Journal of Computational Physics, 52, 24-34 (1983)
     */
    private static final Logger logger = Logger.getLogger(Rattle.class.getName());
  
    private MolecularAssembly molAss;
    private double[] xold;
    private double[] yold;
    private double[] zold;
    private double[][] vel;
    private final int nVariables;
    private final Crystal cryst = molAss.getCrystal();
  
    // set the velocity and original coordinates of global variables in Rattle Class
  
    /**
     * Constructor for Rattle.
     *
     * @param nVariables a int.
     * @param molAss a {@link ffx.potential.MolecularAssembly} object.
     * @param v the initial velocities of the atoms.
     */
    public Rattle(int nVariables, MolecularAssembly molAss, double[] v) {
  
      int i, j = 0;
      Atom[] tempArray = molAss.getAtomArray();
      int size = tempArray.length;
      this.nVariables = nVariables;
  
      // get velocities prior to integrator
      for (i = 0; i < v.length; i = i + 3) {
        this.vel[j][0] = v[i];
        this.vel[j][1] = v[i + 1];
        this.vel[j][2] = v[i + 2];
        j++;
      }
  
      // get coordinates prior to integrator
      for (i = 0; i < size; i++) {
        this.xold[i] = tempArray[i].getX();
        this.yold[i] = tempArray[i].getY();
       this.zold[i] = tempArray[i].getZ();
     }
   }
 
   // Rattle algorithm applied to distances and half-step velocity values
 
   /**
    * postForce1.
    *
    * @param molAss a {@link ffx.potential.MolecularAssembly} object.
    * @param dt a double.
    */
   public void postForce1(MolecularAssembly molAss, double dt) {
     int i, n;
     int niter, maxiter;
     int ia, ib;
     int nrat; // number of bonds Rattle is applied to (all bonds)
     double eps, sor;
     double rateps;
     double xr, yr, zr;
     double xo, yo, zo;
     double dot, rma, rmb;
     double dist2;
     double delta;
     double term;
     double xterm, yterm, zterm;
     double[] xyzr = new double[3];
     double[] xyzo = new double[3];
     boolean done;
 
     n = molAss.getAtomArray().length;
     nrat = molAss.getBondList().size();
 
     // Perform dynamic allocation of some local arrays
     boolean[] moved = new boolean[n];
     boolean[] update = new boolean[n];
     Atom[] atomArray = new Atom[n];
     double[] x = new double[n];
     double[] y = new double[n];
     double[] z = new double[n];
     double[] krat = new double[nrat]; // equilibrium bond length distances
     int[][] bondAtmNum = new int[nrat][2]; // rows correspond with bondArray index
 
     // initialize a list of all bonds in the system
     for (i = 0; i < nrat; i++) {
       bondAtmNum[i][0] = molAss.getBond(i).getAtomArray()[0].getIndex();
       bondAtmNum[i][1] = molAss.getBond(i).getAtomArray()[1].getIndex();
       krat[i] = molAss.getBond(i).bondType.distance; // equilibrium distance
     }
 
     // Initialize the lists of atoms previously corrected
     for (i = 0; i < n; i++) {
       moved[i] = atomArray[i].isActive();
 
       update[i] = false;
     }
 
     // Set the iteration counter, termination and tolerance
     maxiter = 500;
     sor = 1.250;
     rateps = 0.0000010; // default in Tinker
     eps = rateps;
 
     // Apply RATTLE to distances and half-step velocity values
     niter = 0;
     done = false;
 
     while ((!done) && (niter < maxiter)) {
       niter++;
       done = true;
 
       for (i = 0; i < nrat; i++) {
         ia = bondAtmNum[i][0];
         ib = bondAtmNum[i][1];
         if (moved[ia] || moved[ib]) {
           xr = x[ib] - x[ia];
           yr = y[ib] - y[ia];
           zr = z[ib] - z[ia];
           xyzr[0] = xr;
           xyzr[1] = yr;
           xyzr[2] = zr;
 
           dist2 = cryst.image(xyzr);
 
           // update xr, yr, and zr
           xr = xyzr[0];
           yr = xyzr[1];
           zr = xyzr[2];
           delta = (krat[i] * krat[i]) - dist2;
 
           if (abs(delta) > eps) {
             done = false;
             update[ia] = true;
             update[ib] = true;
 
             xo = this.xold[ib] - this.xold[ia];
             yo = this.yold[ib] - this.yold[ia];
             zo = this.zold[ib] - this.zold[ia];
             xyzo[0] = xo;
             xyzo[1] = yo;
             xyzo[2] = zo;
 
             cryst.image(xyzo);
             xo = xyzo[0];
             yo = xyzo[1];
             zo = xyzo[2];
 
             dot = (xr * xo) + (yr * yo) + (zr * zo);
             rma = 1.00 / atomArray[ia].getMass();
             rmb = 1.00 / atomArray[ib].getMass();
             term = sor * delta / (2 * (rma + rmb) * dot);
             xterm = xo * term;
             yterm = yo * term;
             zterm = zo * term;
             // This is where global coordinates should be adjusted
             x[ia] = x[ia] - (xterm * rma);
             y[ia] = y[ia] - (yterm * rma);
             z[ia] = z[ia] - (zterm * rma);
             x[ib] = x[ib] - (xterm * rmb);
             y[ib] = y[ib] - (yterm * rmb);
             z[ib] = z[ib] - (zterm * rmb);
             rma = rma / dt;
             rmb = rmb / dt;
             // This is where global velocity should be adjusted
             this.vel[ia][0] = this.vel[ia][0] - (xterm * rma);
             this.vel[ia][1] = this.vel[ia][1] - (yterm * rma);
             this.vel[ia][2] = this.vel[ia][2] - (zterm * rma);
             this.vel[ib][0] = this.vel[ib][0] - (xterm * rmb);
             this.vel[ib][1] = this.vel[ib][1] - (yterm * rmb);
             this.vel[ib][2] = this.vel[ib][2] - (zterm * rmb);
           }
         }
       }
 
       for (i = 0; i < n; i++) {
         moved[i] = update[i];
         update[i] = false;
       }
     }
 
     // Write information on the number of iterations needed
     if (niter == maxiter) {
       logger.log(Level.SEVERE, "Rattle: Distance constraints not satisfied.\n");
     }
   }
 
   /**
    * postForce2.
    *
    * @param dt a double.
    */
   public void postForce2(double dt) {
     int i, n;
     int ia, ib;
     int niter, maxiter;
     int nrat;
     double eps, sor;
     double xr, yr, zr;
     double xv, yv, zv;
     double dot, rma, rmb;
     double term;
     double xterm, yterm, zterm;
     boolean done;
     double[] xyzr = new double[3];
 
     // Perform dynamic allocation of some local arrays
     n = molAss.getAtomArray().length;
     boolean[] moved = new boolean[n];
     boolean[] update = new boolean[n];
     boolean[] ratimage =
         new boolean
             [molAss.getBondList().size()]; // flag to use minimum image for holonomic constraint
     Atom[] atomArray = new Atom[n];
     int[][] bondAtmNum = new int[molAss.getBondList().size()][2];
     double[] krat = new double[molAss.getBondList().size()];
     double[] x = new double[molAss.getAtomArray().length];
     double[] y = new double[molAss.getAtomArray().length];
     double[] z = new double[molAss.getAtomArray().length];
 
     // initialize a list of all atom coordinates in the system
     n = molAss.getAtomArray().length;
     for (i = 0; i < n; i++) {
       x[i] = atomArray[i].getX();
       y[i] = atomArray[i].getY();
       z[i] = atomArray[i].getZ();
     }
 
     // initialize a list of all bonds in the system
     nrat = molAss.getBondList().size();
     for (i = 0; i < nrat; i++) {
       bondAtmNum[i][0] = molAss.getBond(i).getAtomArray()[0].getIndex();
       bondAtmNum[i][1] = molAss.getBond(i).getAtomArray()[1].getIndex();
       krat[i] = molAss.getBond(i).bondType.distance; // equilibrium distance
     }
 
     // initialize ratimage for minimum image convention
     for (i = 0; i < nrat; i++) {
       ratimage[i] = true;
     }
 
     // initialize lists of atoms previously corrected
     atomArray = molAss.getAtomArray();
     for (i = 0; i < n; i++) {
       moved[i] = atomArray[i].isActive();
 
       update[i] = false;
     }
 
     // set iteration counter, termination, and tolerance
     maxiter = 500;
     niter = 0;
     done = false;
     sor = 1.25;
     eps = 0.000001 / dt;
 
     // apply the RATTLE algorithm to correct velocities
     while ((!done) && (niter < maxiter)) {
       niter++;
       done = true;
       for (i = 1; i < nrat; i++) {
         ia = bondAtmNum[i][0];
         ib = bondAtmNum[i][1];
 
         if (moved[ia] || moved[ib]) {
           xr = x[ib] - x[ia];
           yr = y[ib] - y[ia];
           zr = z[ib] - z[ia];
 
           xyzr[0] = xr;
           xyzr[1] = yr;
           xyzr[2] = zr;
 
           cryst.image(xyzr);
           xr = xyzr[0];
           yr = xyzr[1];
           zr = xyzr[2];
 
           xv = this.vel[ib][0] - this.vel[ia][0];
           yv = this.vel[ib][1] - this.vel[ia][1];
           zv = this.vel[ib][2] - this.vel[ia][2];
           dot = (xr * xv) + (yr * yv) + (zr * zv);
           rma = 1.00 / atomArray[ia].getMass();
           rmb = 1.00 / atomArray[ib].getMass();
           term = -dot / ((rma + rmb) * (krat[i] * krat[i]));
 
           if (abs(term) > eps) {
             done = false;
             update[ia] = true;
             update[ib] = true;
             term = sor * term;
             xterm = xr * term;
             yterm = yr * term;
             zterm = zr * term;
             this.vel[ia][0] = this.vel[ia][0] - (xterm * rma);
             this.vel[ia][1] = this.vel[ia][1] - (yterm * rma);
             this.vel[ia][2] = this.vel[ia][2] - (zterm * rma);
             this.vel[ib][0] = this.vel[ib][0] + (xterm * rma);
             this.vel[ib][1] = this.vel[ib][1] + (yterm * rma);
             this.vel[ib][2] = this.vel[ib][2] + (zterm * rma);
           }
         }
       }
       for (i = 0; i < n; i++) {
         moved[i] = update[i];
         update[i] = false;
       }
     }
 
     // Write information on the number of iterations needed
     if (niter == maxiter) {
       logger.log(Level.SEVERE, "Rattle: Velocity constraints not satisfied.\n");
     }
   }
 }