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
42 import ffx.potential.SystemState;
43 import ffx.numerics.Potential;
44
45 /**
46 * Integrate Newton's equations of motion using a Beeman multistep recursion formula; the actual
47 * coefficients are Brooks' "Better Beeman" values.
48 *
49 * @author Michael J. Schnieders
50 * @since 1.0
51 */
52 public class BetterBeeman extends Integrator {
53
54 private double dt2_8;
55 private double dt_8;
56
57 /**
58 * Constructor for BetterBeeman.
59 *
60 * @param state The current state of the molecular dynamics simulation to operate on.
61 */
62 public BetterBeeman(SystemState state) {
63 super(state);
64 dt_8 = 0.125 * dt;
65 dt2_8 = dt * dt_8;
66 }
67
68 /**
69 * {@inheritDoc}
70 *
71 * <p>Use Newton's second law to get the next acceleration and find the full-step velocities using
72 * the Beeman recursion.
73 */
74 @Override
75 public void postForce(double[] gradient) {
76 copyAccelerationToPrevious();
77 double[] a = state.a();
78 double[] v = state.v();
79 double[] mass = state.getMass();
80 double[] aPrevious = state.aPrevious();
81 for (int i = 0; i < state.getNumberOfVariables(); i++) {
82 double m = mass[i];
83 if (m > 0.0) {
84 a[i] = -KCAL_TO_GRAM_ANG2_PER_PS2 * gradient[i] / m;
85 v[i] += (3.0 * a[i] + aPrevious[i]) * dt_8;
86 }
87 }
88 }
89
90 /**
91 * {@inheritDoc}
92 *
93 * <p>Store the current atom positions, then find new atom positions and half-step velocities via
94 * Beeman recursion.
95 */
96 @Override
97 public void preForce(Potential potential) {
98 double[] x = state.x();
99 double[] a = state.a();
100 double[] v = state.v();
101 double[] mass = state.getMass();
102 double[] aPrevious = state.aPrevious();
103 for (int i = 0; i < state.getNumberOfVariables(); i++) {
104 double m = mass[i];
105 if (m > 0.0) {
106 double temp = 5.0 * a[i] - aPrevious[i];
107 x[i] += v[i] * dt + temp * dt2_8;
108 v[i] += temp * dt_8;
109 }
110 }
111 }
112
113 /** {@inheritDoc} */
114 @Override
115 public void setTimeStep(double dt) {
116 this.dt = dt;
117 dt_8 = 0.125 * dt;
118 dt2_8 = dt * dt_8;
119 }
120
121 /** {@inheritDoc} */
122 @Override
123 public String toString() {
124 return "Better Beeman";
125 }
126 }