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.potential.openmm;
39
40 import ffx.openmm.Integrator;
41 import ffx.openmm.LangevinIntegrator;
42 import ffx.openmm.VerletIntegrator;
43 import ffx.potential.parameters.ForceField;
44 import org.apache.commons.configuration2.CompositeConfiguration;
45
46 import java.util.logging.Logger;
47
48 import static ffx.potential.ForceFieldEnergy.DEFAULT_CONSTRAINT_TOLERANCE;
49 import static java.lang.String.format;
50
51 /**
52 * Create and manage an OpenMM Integrator.
53 *
54 * <p>An Integrator defines a method for simulating a System by integrating the equations of
55 * motion.
56 *
57 * <p>Each Integrator object is bound to a particular Context which it integrates. This connection
58 * is specified by passing the Integrator as an argument to the constructor of the Context.
59 */
60 public class OpenMMIntegrator {
61
62 private static final Logger logger = Logger.getLogger(OpenMMIntegrator.class.getName());
63
64 /**
65 * Constraint tolerance as a fraction of the constrained bond length.
66 */
67 private final static double constraintTolerance = DEFAULT_CONSTRAINT_TOLERANCE;
68
69 /**
70 * Prevent instantiation.
71 */
72 private OpenMMIntegrator() {
73
74 }
75
76 /**
77 * Create a integrator.
78 *
79 * @param name Name of the integrator to use.
80 * @param timeStep Time step (psec).
81 * @param temperature Target temperature (kelvin).
82 * @param openMMSystem OpenMM System.
83 * @return Integrator reference.
84 */
85 public static Integrator createIntegrator(String name, double timeStep, double temperature, OpenMMSystem openMMSystem) {
86 switch (name) {
87 default -> {
88 return createVerletIntegrator(timeStep);
89 }
90 case "LANGEVIN" -> {
91 return createLangevinIntegrator(timeStep, temperature, openMMSystem.getForceField());
92 }
93 case "MTS" -> {
94 return createCustomMTSIntegrator(timeStep, openMMSystem);
95 }
96 case "LANGEVIN-MTS" -> {
97 return createCustomMTSLangevinIntegrator(timeStep, temperature, openMMSystem);
98 }
99 }
100 }
101
102 /**
103 * Create a Langevin integrator.
104 *
105 * @param dt Time step (psec).
106 * @param temperature Temperature (K).
107 * @param forceField Force field.
108 */
109 public static LangevinIntegrator createLangevinIntegrator(double dt, double temperature, ForceField forceField) {
110 CompositeConfiguration properties = forceField.getProperties();
111 int seed = 0;
112 if (properties.containsKey("integrator-seed")) {
113 seed = properties.getInt("integrator-seed", 0);
114 }
115 double frictionCoeff = forceField.getDouble("FRICTION_COEFF", 91.0);
116 LangevinIntegrator langevinIntegrator = new LangevinIntegrator(dt, temperature, frictionCoeff);
117 langevinIntegrator.setRandomNumberSeed(seed);
118 langevinIntegrator.setConstraintTolerance(constraintTolerance);
119 logger.info(" Langevin Integrator");
120 logger.info(format(" Target Temperature: %6.2f (K)", temperature));
121 logger.info(format(" Friction Coefficient: %6.2f (1/psec)", frictionCoeff));
122 logger.info(format(" Time step: %6.2f (fsec)", dt * 1000));
123 return langevinIntegrator;
124 }
125
126 /**
127 * Create a Custom MTS Integrator.
128 *
129 * @param dt The outer time step (psec).
130 */
131 public static CustomMTSIntegrator createCustomMTSIntegrator(double dt, OpenMMSystem openMMSystem) {
132 return new CustomMTSIntegrator(dt, constraintTolerance, openMMSystem.hasAmoebaCavitationForce());
133 }
134
135
136 /**
137 * Create a Custom MTS Langevin integrator.
138 *
139 * @param dt The outer time step (psec).
140 * @param temperature The target temperature (K).
141 * @param openMMSystem OpenMM System.
142 */
143 public static CustomMTSLangevinIntegrator createCustomMTSLangevinIntegrator(double dt, double temperature, OpenMMSystem openMMSystem) {
144
145 ForceField forceField = openMMSystem.getForceField();
146 double frictionCoeff = forceField.getDouble("FRICTION_COEFF", 91.0);
147 CustomMTSLangevinIntegrator customMTSLangevinIntegrator =
148 new CustomMTSLangevinIntegrator(dt, temperature, frictionCoeff, openMMSystem.hasAmoebaCavitationForce());
149 return customMTSLangevinIntegrator;
150 }
151
152 /**
153 * Create a Verlet integrator.
154 *
155 * @param dt Time step (psec).
156 */
157 public static VerletIntegrator createVerletIntegrator(double dt) {
158 VerletIntegrator verletIntegrator = new VerletIntegrator(dt);
159 verletIntegrator.setConstraintTolerance(constraintTolerance);
160 logger.info(" Verlet Integrator");
161 logger.info(format(" Time step: %6.2f (fsec)", dt * 1000));
162 return verletIntegrator;
163 }
164
165 }