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.dynamics.MolecularDynamics;
43 import ffx.algorithms.misc.AlgorithmsTest;
44 import java.util.Arrays;
45 import java.util.Collection;
46 import org.junit.Test;
47 import org.junit.runner.RunWith;
48 import org.junit.runners.Parameterized;
49 import org.junit.runners.Parameterized.Parameters;
50
51 /** @author Hernan V Bernabe */
52 @RunWith(Parameterized.class)
53 public class DynamicsBeemanBerendsenTest extends AlgorithmsTest {
54
55 private String info;
56 private String filename;
57 private double endKineticEnergy;
58 private double endPotentialEnergy;
59 private double endTotalEnergy;
60 private double endTemperature;
61 private double tolerance = 0.1;
62
63 public DynamicsBeemanBerendsenTest(
64 String info,
65 String filename,
66 double endKineticEnergy,
67 double endPotentialEnergy,
68 double endTotalEnergy,
69 double endTemperature) {
70 this.info = info;
71 this.filename = filename;
72 this.endKineticEnergy = endKineticEnergy;
73 this.endPotentialEnergy = endPotentialEnergy;
74 this.endTotalEnergy = endTotalEnergy;
75 this.endTemperature = endTemperature;
76 }
77
78 @Parameters
79 public static Collection<Object[]> data() {
80 return Arrays.asList(
81 new Object[][] {
82 {
83 "Acetamide with BetterBeeman Integrator and Berendsen Thermostat", // info
84 "acetamide_NVE.xyz", // filename
85 4.8087, // endKineticEnergy
86 -29.7186, // endPotentialEnergy
87 -24.9099, // endTotalEnergy
88 201.65 // End temperature
89 }
90 });
91 }
92
93 @Test
94 public void testDynamicsBeemanBerendsen() {
95
96 String filepath = getResourcePath(filename);
97
98 // Set-up the input arguments for the script.
99 String[] args = {
100 "-n", "10",
101 "-t", "298.15",
102 "-i", "Beeman",
103 "-b", "Berendsen",
104 "-r", "0.001",
105 filepath
106 };
107 binding.setVariable("args", args);
108
109 // Construct and evaluate the script.
110 Dynamics dynamics = new Dynamics(binding).run();
111 algorithmsScript = dynamics;
112 MolecularDynamics molDyn = dynamics.getMolecularDynamics();
113
114 // Assert that end energies are within the tolerance for the dynamics trajectory
115 assertEquals(info + " Final kinetic energy", endKineticEnergy, molDyn.getKineticEnergy(), tolerance);
116 assertEquals(info + " Final potential energy", endPotentialEnergy, molDyn.getPotentialEnergy(), tolerance);
117 assertEquals(info + " Final total energy", endTotalEnergy, molDyn.getTotalEnergy(), tolerance);
118 assertEquals(info + " Final temperature", endTemperature, molDyn.getTemperature(), tolerance);
119 }
120 }