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.cli;
39
40 import picocli.CommandLine.ArgGroup;
41 import picocli.CommandLine.Option;
42
43 /**
44 * Represents command line options for scripts that utilize a mobile lambda particle, such as
45 * Thermodynamics.
46 *
47 * @author Michael J. Schnieders
48 * @author Jacob M. Litman
49 * @since 1.0
50 */
51 public class LambdaParticleOptions {
52
53 /**
54 * The default theta friction is 91 per psec.
55 */
56 private static final double DEFAULT_THETA_FRICTION = 91.0;
57
58 /**
59 * The default theta mass is 10 AMU.
60 */
61 private static final double DEFAULT_THETA_MASS = 10.0;
62
63 /**
64 * The ArgGroup keeps the LambdaParticleOptions together when printing help.
65 */
66 @ArgGroup(heading = "%n Lambda Particle Options for MD-OST%n", validate = false)
67 private final LambdaParticleOptionGroup group = new LambdaParticleOptionGroup();
68
69 /**
70 * Friction on the lambda particle.
71 *
72 * @return a double.
73 */
74 public double getLambdaFriction() {
75 return group.lambdaFriction;
76 }
77
78 public void setLambdaFriction(double lambdaFriction) {
79 group.lambdaFriction = lambdaFriction;
80 }
81
82 /**
83 * The mass of the lambda particle.
84 *
85 * @return a double.
86 */
87 public double getLambdaMass() {
88 return group.lambdaMass;
89 }
90
91 public void setLambdaMass(double lambdaMass) {
92 group.lambdaMass = lambdaMass;
93 }
94
95 /**
96 * Collection of Lambda Particle Options.
97 */
98 private static class LambdaParticleOptionGroup {
99
100 /**
101 * -m or --lambdaMass to set the mass of the lambda particle.
102 */
103 @Option(names = {"--lm", "--lambdaMass"}, paramLabel = "" + DEFAULT_THETA_MASS, defaultValue = "" + DEFAULT_THETA_MASS,
104 description = "Mass of the lambda particle (AMU).")
105 private double lambdaMass = DEFAULT_THETA_MASS;
106
107 /**
108 * -x or --lambdaFriction to set the friction on the lambda particle.
109 */
110 @Option(names = {"--lf", "--lambdaFriction"}, paramLabel = "" + DEFAULT_THETA_FRICTION, defaultValue = "" + DEFAULT_THETA_FRICTION,
111 description = "Friction on the lambda particle (1/psec).")
112 private double lambdaFriction = DEFAULT_THETA_FRICTION;
113 }
114 }