1 // ******************************************************************************
2 //
3 // Title: Force Field X.
4 // Description: Force Field X - Software for Molecular Biophysics.
5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2025.
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
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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.commands;
39
40 import ffx.algorithms.misc.AlgorithmsTest;
41 import org.junit.Test;
42
43 import static org.junit.Assert.assertEquals;
44
45 /**
46 * Tests CrystalMin and CrystalMin.groovy scripts for -e -I -f and -c flags.
47 *
48 * @author Aaron J. Nessler
49 * @author Mallory R. Tollefson
50 */
51 public class MinimizeCrystalsTest extends AlgorithmsTest {
52
53 /**
54 * Tests convergence criteria flag of the CrystalMin class.
55 */
56 @Test
57 public void testCrystalMinConvergenceCriteria() {
58 // Set-up the input arguments for the script.
59 String[] args = {"-e", "0.25", "-f", "molecule", getResourcePath("acetamide.xtal.xyz")};
60 binding.setVariable("args", args);
61 binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
62
63 // Construct and evaluate the script.
64 MinimizeCrystals xtalMin = new MinimizeCrystals(binding).run();
65 algorithmsScript = xtalMin;
66
67 double expectedPotentialEnergy = -32.72658281436831;
68 double actualPotentialEnergy =
69 xtalMin.getPotentials().get(xtalMin.getPotentials().size() - 1).getTotalEnergy();
70 assertEquals(expectedPotentialEnergy, actualPotentialEnergy, 1E-6);
71 }
72
73 /**
74 * Tests the fractional flag of the CrystalMin class.
75 */
76 @Test
77 public void testCrystalMinCoords() {
78 // Set-up the input arguments for the script.
79 String[] args = {"-c", "-f", "molecule", getResourcePath("acetamide.xtal.xyz")};
80 binding.setVariable("args", args);
81 binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
82
83 // Construct and evaluate the script.
84 MinimizeCrystals xtalMin = new MinimizeCrystals(binding).run();
85 algorithmsScript = xtalMin;
86
87 double expectedPotentialEnergy = -32.53569940765405;
88
89 double actualPotentialEnergy =
90 xtalMin.getPotentials().get(xtalMin.getPotentials().size() - 1).getTotalEnergy();
91 assertEquals(expectedPotentialEnergy, actualPotentialEnergy, 1E-6);
92 }
93
94 /**
95 * Tests the fractional flag of the CrystalMin class.
96 */
97 @Test
98 public void testCrystalMinFractional() {
99 // Set-up the input arguments for the script.
100 String[] args = {"-f", "ATOM", "-e", "0.24", getResourcePath("acetamide.xtal.xyz")};
101 binding.setVariable("args", args);
102 binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
103
104 // Construct and evaluate the script.
105 MinimizeCrystals xtalMin = new MinimizeCrystals(binding).run();
106 algorithmsScript = xtalMin;
107
108 double expectedPotentialEnergy = -32.54443798845555;
109
110 double actualPotentialEnergy =
111 xtalMin.getPotentials().get(xtalMin.getPotentials().size() - 1).getTotalEnergy();
112 assertEquals(expectedPotentialEnergy, actualPotentialEnergy, 1E-6);
113 }
114
115 @Test
116 public void testCrystalMinHelp() {
117 // Set-up the input arguments for the CrystalMin script.
118 String[] args = {"-h"};
119 binding.setVariable("args", args);
120
121 // Construct and evaluate the script.
122 MinimizeCrystals xtalMin = new MinimizeCrystals(binding).run();
123 algorithmsScript = xtalMin;
124 }
125
126 /**
127 * Tests the iterations flag of the CrystalMin class.
128 */
129 @Test
130 public void testCrystalMinIterations() {
131 // Set-up the input arguments for the script.
132 String[] args = {"-I", "1", "-e", "0.25", "-f", "molecule", getResourcePath("acetamide.xtal.xyz")};
133
134 binding.setVariable("args", args);
135 binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
136
137 // Construct and evaluate the script.
138 MinimizeCrystals xtalMin = new MinimizeCrystals(binding).run();
139 algorithmsScript = xtalMin;
140
141 double expectedPotentialEnergy = -32.63131694976352;
142
143 double actualPotentialEnergy =
144 xtalMin.getPotentials().get(xtalMin.getPotentials().size() - 1).getTotalEnergy();
145 assertEquals(expectedPotentialEnergy, actualPotentialEnergy, 1E-6);
146 }
147 }