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.cli;
39
40 import picocli.CommandLine.ArgGroup;
41 import picocli.CommandLine.Option;
42
43 /**
44 * Represents command line options for scripts that test gradients.
45 *
46 * @author Michael J. Schnieders
47 * @since 1.0
48 */
49 public class GradientOptions {
50
51 /**
52 * The ArgGroup keeps the GradientOptions together when printing help.
53 */
54 @ArgGroup(heading = "%n Gradient Options%n", validate = false)
55 private final GradientOptionGroup group = new GradientOptionGroup();
56
57 /**
58 * -d or --dx Finite-difference step size.
59 *
60 * @return Returns the Finite-difference step size.
61 */
62 public double getDx() {
63 return group.dx;
64 }
65
66 /**
67 * --tol or --tolerance Gradient error tolerance (kcal/mol/Å).
68 *
69 * @return Returns the gradient error tolerance.
70 */
71 public double getTolerance() {
72 return group.tolerance;
73 }
74
75 /**
76 * --ga or --gradientAtoms Ranges of atoms to test [ALL, NONE, Range(s): 1-3,6-N].
77 *
78 * @return Returns the ranges of atoms to test.
79 */
80 public String getGradientAtoms() {
81 return group.gradientAtoms;
82 }
83
84 /**
85 * -v or --verbose is a flag to print out energy at each step.
86 *
87 * @return Returns true to print out energy at each step.
88 */
89 public boolean getVerbose() {
90 return group.verbose;
91 }
92
93 /**
94 * Collection of Gradient Options.
95 */
96 private static class GradientOptionGroup {
97
98 /**
99 * -d or --dx Finite-difference step size.
100 */
101 @Option(names = {"-d", "--dx"}, defaultValue = "1.0e-5", paramLabel = "1.0e-5 Å",
102 description = "Finite-difference step size.")
103 public double dx = 1.0e-5;
104
105 /**
106 * --tol or --tolerance Gradient error tolerance (kcal/mol/Å).
107 */
108 @Option(names = {"--tol", "--tolerance"}, defaultValue = "1.0e-3",
109 paramLabel = "1.0e-3 kcal/mol/Å", description = "Gradient error tolerance.")
110 public double tolerance = 1.0e-3;
111
112 /**
113 * --ga or --gradientAtoms Ranges of degrees of freedom to test [ALL, NONE, Range(s): 1-3,6-N].
114 */
115 @Option(names = {"--ga", "--gradientAtoms"}, paramLabel = "ALL", defaultValue = "ALL",
116 description = "Ranges of degrees of freedom to test [ALL, NONE, Range(s): 1-3,6-N].")
117 public String gradientAtoms = "ALL";
118
119 /**
120 * -v or --verbose is a flag to print out energy at each step.
121 */
122 @Option(names = {"-v", "--verbose"}, paramLabel = "false",
123 description = "Print out the energy for each step.")
124 public boolean verbose = false;
125 }
126
127 }