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 DynamicsInitVelocitiesTest extends AlgorithmsTest {
54
55 private String info;
56 private String filename;
57 private double endKineticEnergy;
58 private double kineticEnergyTolerance = 5.0;
59 private double endPotentialEnergy;
60 private double potentialEnergyTolerance = 5.0;
61 private double endTotalEnergy;
62 private double totalEnergyTolerance = 5.0;
63
64 public DynamicsInitVelocitiesTest(
65 String info,
66 String filename,
67 double endKineticEnergy,
68 double endPotentialEnergy,
69 double endTotalEnergy) {
70
71 this.info = info;
72 this.filename = filename;
73 this.endKineticEnergy = endKineticEnergy;
74 this.endPotentialEnergy = endPotentialEnergy;
75 this.endTotalEnergy = endTotalEnergy;
76 }
77
78 @Parameters
79 public static Collection<Object[]> data() {
80 return Arrays.asList(
81 new Object[][] {
82 {
83 "Water Tiny Initialize Velocities", // info
84 "watertiny.xyz", // filename
85 64.8511, // endKineticEnergy
86 -218.0760, // endPotentialEnergy
87 -153.2249 // endTotalEnergy
88 }
89 });
90 }
91
92 @Test
93 public void testDynamicsInitVelocities() {
94
95 // Set-up the input arguments for the script.
96 String[] args = {
97 "-n", "10",
98 "-t", "298.15",
99 "-i", "VelocityVerlet",
100 "-b", "Adiabatic",
101 "-r", "0.001",
102 getResourcePath(filename)
103 };
104 binding.setVariable("args", args);
105
106 // Construct and evaluate the script.
107 Dynamics dynamics = new Dynamics(binding).run();
108 algorithmsScript = dynamics;
109
110 MolecularDynamics molDyn = dynamics.getMolecularDynamics();
111
112 // Assert that final energies are within the tolerance for the dynamics trajectory.
113 assertEquals(
114 info + "End kinetic energy for initializing velocities test",
115 endKineticEnergy,
116 molDyn.getKineticEnergy(),
117 kineticEnergyTolerance);
118
119 assertEquals(
120 info + "End potential energy for initializing velocities test",
121 endPotentialEnergy,
122 molDyn.getPotentialEnergy(),
123 potentialEnergyTolerance);
124
125 assertEquals(
126 info + "End total energy for initializing velocities test",
127 endTotalEnergy,
128 molDyn.getTotalEnergy(),
129 totalEnergyTolerance);
130 }
131 }