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.groovy;
39
40 import static org.junit.Assert.assertEquals;
41
42 import ffx.algorithms.misc.AlgorithmsTest;
43 import org.junit.Test;
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 /** Tests convergence criteria flag of the CrystalMin class. */
54 @Test
55 public void testCrystalMinConvergenceCriteria() {
56 // Set-up the input arguments for the script.
57 String[] args = {"-e", "0.25", getResourcePath("acetamide.xtal.xyz")};
58 binding.setVariable("args", args);
59 binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
60
61 // Construct and evaluate the script.
62 MinimizeCrystals xtalMin = new MinimizeCrystals(binding).run();
63 algorithmsScript = xtalMin;
64
65 double expectedPotentialEnergy = -32.72657973215976;
66
67 double actualPotentialEnergy =
68 xtalMin.getPotentials().get(xtalMin.getPotentials().size() - 1).getTotalEnergy();
69 assertEquals(expectedPotentialEnergy, actualPotentialEnergy, 1E-6);
70 }
71
72 /** Tests the fractional flag of the CrystalMin class. */
73 @Test
74 public void testCrystalMinCoords() {
75 // Set-up the input arguments for the script.
76 String[] args = {"-c", getResourcePath("acetamide.xtal.xyz")};
77 binding.setVariable("args", args);
78 binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
79
80 // Construct and evaluate the script.
81 MinimizeCrystals xtalMin = new MinimizeCrystals(binding).run();
82 algorithmsScript = xtalMin;
83
84 double expectedPotentialEnergy = -32.53569940765405;
85
86 double actualPotentialEnergy =
87 xtalMin.getPotentials().get(xtalMin.getPotentials().size() - 1).getTotalEnergy();
88 assertEquals(expectedPotentialEnergy, actualPotentialEnergy, 1E-6);
89 }
90
91 /** Tests the fractional flag of the CrystalMin class. */
92 @Test
93 public void testCrystalMinFractional() {
94 // Set-up the input arguments for the script.
95 String[] args = {"-f", "ATOM", "-e", "0.24", getResourcePath("acetamide.xtal.xyz")};
96 binding.setVariable("args", args);
97 binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
98
99 // Construct and evaluate the script.
100 MinimizeCrystals xtalMin = new MinimizeCrystals(binding).run();
101 algorithmsScript = xtalMin;
102
103 double expectedPotentialEnergy = -32.54443451197122;
104
105 double actualPotentialEnergy =
106 xtalMin.getPotentials().get(xtalMin.getPotentials().size() - 1).getTotalEnergy();
107 assertEquals(expectedPotentialEnergy, actualPotentialEnergy, 1E-6);
108 }
109
110 @Test
111 public void testCrystalMinHelp() {
112 // Set-up the input arguments for the CrystalMin script.
113 String[] args = {"-h"};
114 binding.setVariable("args", args);
115
116 // Construct and evaluate the script.
117 MinimizeCrystals xtalMin = new MinimizeCrystals(binding).run();
118 algorithmsScript = xtalMin;
119 }
120
121 /** Tests the iterations flag of the CrystalMin class. */
122 @Test
123 public void testCrystalMinIterations() {
124 // Set-up the input arguments for the script.
125 String[] args = {"-I", "1", "-e", "0.25", getResourcePath("acetamide.xtal.xyz")};
126
127 binding.setVariable("args", args);
128 binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
129
130 // Construct and evaluate the script.
131 MinimizeCrystals xtalMin = new MinimizeCrystals(binding).run();
132 algorithmsScript = xtalMin;
133
134 double expectedPotentialEnergy = -32.63131283241016;
135
136 double actualPotentialEnergy =
137 xtalMin.getPotentials().get(xtalMin.getPotentials().size() - 1).getTotalEnergy();
138 assertEquals(expectedPotentialEnergy, actualPotentialEnergy, 1E-6);
139 }
140 }