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1   // ******************************************************************************
2   //
3   // Title:       Force Field X.
4   // Description: Force Field X - Software for Molecular Biophysics.
5   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2024.
6   //
7   // This file is part of Force Field X.
8   //
9   // Force Field X is free software; you can redistribute it and/or modify it
10  // under the terms of the GNU General Public License version 3 as published by
11  // the Free Software Foundation.
12  //
13  // Force Field X is distributed in the hope that it will be useful, but WITHOUT
14  // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
15  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
16  // details.
17  //
18  // You should have received a copy of the GNU General Public License along with
19  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
20  // Place, Suite 330, Boston, MA 02111-1307 USA
21  //
22  // Linking this library statically or dynamically with other modules is making a
23  // combined work based on this library. Thus, the terms and conditions of the
24  // GNU General Public License cover the whole combination.
25  //
26  // As a special exception, the copyright holders of this library give you
27  // permission to link this library with independent modules to produce an
28  // executable, regardless of the license terms of these independent modules, and
29  // to copy and distribute the resulting executable under terms of your choice,
30  // provided that you also meet, for each linked independent module, the terms
31  // and conditions of the license of that module. An independent module is a
32  // module which is not derived from or based on this library. If you modify this
33  // library, you may extend this exception to your version of the library, but
34  // you are not obligated to do so. If you do not wish to do so, delete this
35  // exception statement from your version.
36  //
37  // ******************************************************************************
38  package ffx.algorithms.dynamics.integrators;
39  
40  import static ffx.utilities.Constants.KCAL_TO_GRAM_ANG2_PER_PS2;
41  import static java.lang.System.arraycopy;
42  import static java.util.Arrays.copyOf;
43  
44  import ffx.potential.SystemState;
45  import ffx.numerics.Constraint;
46  import ffx.numerics.Potential;
47  
48  /**
49   * Integrate Newton's equations of motion using a Velocity Verlet multistep recursion formula.
50   *
51   * @author Michael J. Schnieders
52   * @since 1.0
53   */
54  public class VelocityVerlet extends Integrator {
55  
56    private double[] xPrior;
57  
58    /**
59     * Constructor for VelocityVerlet.
60     *
61     * @param state The current state of the molecular dynamics simulation to operate on.
62     */
63    public VelocityVerlet(SystemState state) {
64      super(state);
65    }
66  
67    /**
68     * {@inheritDoc}
69     *
70     * <p>Use Newton's second law to find accelerations and then full-step velocities.
71     */
72    @Override
73    public void postForce(double[] gradient) {
74      copyAccelerationToPrevious();
75      double[] a = state.a();
76      // double[] aPrevious = state.aPrevious();
77      double[] v = state.v();
78      double[] x = state.x();
79      double[] mass = state.getMass();
80      for (int i = 0; i < state.getNumberOfVariables(); i++) {
81        double m = mass[i];
82        if (m > 0.0) {
83          a[i] = -KCAL_TO_GRAM_ANG2_PER_PS2 * gradient[i] / mass[i];
84          v[i] = v[i] + a[i] * dt_2;
85        }
86      }
87      constraints.forEach((Constraint c) -> c.applyConstraintToVelocities(x, v, mass, constraintTolerance));
88    }
89  
90    /**
91     * {@inheritDoc}
92     *
93     * <p>Find half-step velocities and full-step positions.
94     */
95    @Override
96    public void preForce(Potential potential) {
97      double[] x = state.x();
98      double[] v = state.v();
99      double[] a = state.a();
100     double[] mass = state.getMass();
101     int nVariables = state.getNumberOfVariables();
102     if (useConstraints) {
103       if (xPrior == null) {
104         xPrior = copyOf(x, nVariables);
105       } else {
106         arraycopy(x, 0, xPrior, 0, nVariables);
107       }
108     }
109     for (int i = 0; i < nVariables; i++) {
110       double m = mass[i];
111       if (m > 0.0) {
112         v[i] = v[i] + a[i] * dt_2;
113         x[i] = x[i] + v[i] * dt;
114       }
115     }
116     if (useConstraints) {
117       constraints.forEach((Constraint c) -> c.applyConstraintToStep(xPrior, x, mass, constraintTolerance));
118       double velScale = 1.0 / dt;
119       for (int i = 0; i < nVariables; i++) {
120         double m = mass[i];
121         if (m > 0.0) {
122           v[i] = velScale * (x[i] - xPrior[i]);
123         }
124       }
125     }
126   }
127 
128   /** {@inheritDoc} */
129   @Override
130   public void setTimeStep(double dt) {
131     this.dt = dt;
132     dt_2 = dt * 0.5;
133   }
134 
135   /** {@inheritDoc} */
136   @Override
137   public String toString() {
138     return "Velocity Verlet";
139   }
140 }