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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 DynamicsRESPANVETest extends AlgorithmsTest {
54  
55    private String info;
56    private String filename;
57    private double startingTotalEnergy;
58    // Tight tolerance on energy conservation.
59    private double tolerance = 0.01;
60  
61    public DynamicsRESPANVETest(String info, String filename, double startingTotalEnergy) {
62      this.info = info;
63      this.filename = filename;
64      this.startingTotalEnergy = startingTotalEnergy;
65    }
66  
67    @Parameters
68    public static Collection<Object[]> data() {
69      return Arrays.asList(
70          new Object[][] {
71              {
72                  "Acetamide RESPA NVE", // info
73                  "acetamide_NVE.xyz", // filename
74                  -25.2085 // startingTotalEnergy
75              }
76          });
77    }
78  
79    @Test
80    public void testRESPANVE() {
81  
82      // Set-up the input arguments for the script.
83      String[] args = {
84          "-n", "20",
85          "--dt", "0.5",
86          "-t", "298.15",
87          "-i", "RESPA",
88          "-b", "Adiabatic",
89          "-r", "0.001",
90          getResourcePath(filename)
91      };
92      binding.setVariable("args", args);
93  
94      // Construct and evaluate the script.
95      Dynamics dynamics = new Dynamics(binding).run();
96      algorithmsScript = dynamics;
97  
98      MolecularDynamics molDyn = dynamics.getMolecularDynamics();
99  
100     // Assert that the final total energy is within the tolerance for the molecular dynamics
101     // trajectory
102     assertEquals(
103         info + "End total energy for RESPA integrator NVE",
104         startingTotalEnergy,
105         molDyn.getTotalEnergy(),
106         tolerance);
107   }
108 }