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 }