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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.xray;
39  
40  import static org.junit.Assert.assertEquals;
41  
42  import ffx.algorithms.misc.AlgorithmsTest;
43  import ffx.numerics.Potential;
44  import ffx.xray.groovy.ManyBody;
45  import java.util.List;
46  import org.junit.Test;
47  
48  /**
49   * Tests X-Ray many body optimization and the X-Ray many body groovy script under varying
50   * parameters.
51   *
52   * @author Mallory R. Tollefson
53   */
54  public class XRayManyBodyTest extends AlgorithmsTest {
55  
56    // @Test
57    public void testManyBodyGlobal() {
58      // Set-up the input arguments for the script.
59      String[] args = {
60          "-a", "2",
61          "-L", "2",
62          "--sR", "1",
63          "--fR", "5",
64          getResourcePath("5awl.pdb"),
65          getResourcePath("5awl.mtz")
66      };
67      binding.setVariable("args", args);
68      binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
69  
70      // Construct and evaluate the ManyBody script.
71      ManyBody manyBody = new ManyBody(binding).run();
72      algorithmsScript = manyBody;
73  
74      List<Potential> list = manyBody.getPotentials();
75      double expectedPotential = 35106.252654189106;
76      double actualPotential = list.get(0).getTotalEnergy();
77      double tol = 1.0E-4 * expectedPotential;
78      assertEquals(expectedPotential, actualPotential, tol);
79      manyBody.getManyBodyOptions().getRestartFile().delete();
80    }
81  
82    @Test
83    public void testManyBodyHelp() {
84      // Set-up the input arguments for the Biotype script.
85      String[] args = {"-h"};
86      binding.setVariable("args", args);
87  
88      // Construct and evaluate the ManyBody script.
89      ManyBody manyBody = new ManyBody(binding).run();
90      algorithmsScript = manyBody;
91    }
92  }