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.openmm;
39
40 import com.sun.jna.ptr.PointerByReference;
41
42 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Integrator_destroy;
43 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Integrator_setConstraintTolerance;
44 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Integrator_step;
45
46 /**
47 * An Integrator defines a method for simulating a System by integrating the equations of motion.
48 * This is an abstract class. Subclasses define particular integration methods.
49 * <p>
50 * Each Integrator object is bound to a particular Context which it integrates. This connection
51 * is specified by passing the Integrator as an argument to the constructor of the Context.
52 */
53
54 public abstract class Integrator {
55
56 /**
57 * OpenMM Integrator pointer.
58 */
59 protected PointerByReference pointer;
60
61 /**
62 * Constructor.
63 */
64 public Integrator() {
65 pointer = null;
66 }
67
68 /**
69 * Set the OpenMM Integrator pointer.
70 *
71 * @param pointer The OpenMM Integrator pointer.
72 */
73 public void setPointer(PointerByReference pointer) {
74 this.pointer = pointer;
75 }
76
77 /**
78 * Get the OpenMM Integrator pointer.
79 *
80 * @return The OpenMM Integrator pointer.
81 */
82 public PointerByReference getPointer() {
83 return pointer;
84 }
85
86 /**
87 * Integrate the system forward in time by the specified number of time steps.
88 *
89 * @param steps The number of steps to take.
90 */
91 public void step(int steps) {
92 OpenMM_Integrator_step(pointer, steps);
93 }
94
95 /**
96 * Set the tolerance within which constraints must be satisfied during the
97 * simulation. The default value is 1e-5 nm.
98 *
99 * @param tolerance The tolerance within which constraints must be satisfied.
100 */
101 public void setConstraintTolerance(double tolerance) {
102 OpenMM_Integrator_setConstraintTolerance(pointer, tolerance);
103 }
104
105 /**
106 * This method will be called by subclasses when the integrator is destroyed.
107 */
108 public void destroy() {
109 if (pointer != null) {
110 OpenMM_Integrator_destroy(pointer);
111 pointer = null;
112 }
113 }
114
115 }