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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 2001-2025.
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 ffx.algorithms.misc.AlgorithmsTest;
41  import ffx.numerics.estimator.FreeEnergyDifferenceReporter;
42  import org.junit.Assert;
43  import org.junit.Test;
44  
45  public class BARSingleTopologyTest extends AlgorithmsTest {
46  
47    /**
48     * Tests BAR script with nw input.
49     */
50    //@Test
51    public void testBAR() {
52  
53      if (!ffxOpenMM) {
54        return;
55      }
56  
57      // Set-up the input arguments for the script.
58      String filepath = getResourcePath("testBar/singleTopology/dimethylphosphate.10.xyz");
59      String[] args = {"-t", "298", "--nw", "8", "--ac", "1-13", filepath};
60      binding.setVariable("args", args);
61      // Evaluate the script.
62      BAR bar = new BAR(binding).run();
63      algorithmsScript = bar;
64  
65      FreeEnergyDifferenceReporter reporter = bar.getReporter();
66  
67      double expectedFepFor = -54.3012;
68      double actualFepFor = reporter.getForwardTotalFEDifference();
69      Assert.assertEquals(expectedFepFor, actualFepFor, 0.2);
70  
71      double expectedFepBack = -52.9186;
72      double actualFepBack = reporter.getBackwardTotalFEDifference();
73      Assert.assertEquals(expectedFepBack, actualFepBack, 0.2);
74  
75      double expectedhFor = -32.0327;
76      double actualhFor = reporter.getForwardTotalEnthalpyChange();
77      Assert.assertEquals(expectedhFor, actualhFor, 7);
78  
79      double expectedhBack = 52.9186;
80      double actualhBack = reporter.getBackwardTotalEnthalpyChange();
81      Assert.assertEquals(expectedhBack, actualhBack, 0.1);
82  
83      double expectedhBAR = 14.6302;
84      double actualhBAR = reporter.getBarBSTotalEnthalpyChange();
85      Assert.assertEquals(expectedhBAR, actualhBAR, 1);
86  
87      double expectedBARIteration = -53.3234;
88      double actualBARIteration = reporter.getBarIterTotalFEDiff();
89      Assert.assertEquals(expectedBARIteration, actualBARIteration, 0.1);
90  
91      double expectedBARBootstrap = -53.3224;
92      double actualBARBootstrap = reporter.getBarBSTotalFEDiff();
93      Assert.assertEquals(expectedBARBootstrap, actualBARBootstrap, 0.2);
94    }
95  
96    @Test
97    public void testBARHelp() {
98      String[] args = {"-h"};
99      binding.setVariable("args", args);
100 
101     // Evaluate the script.
102     BAR bar = new BAR(binding).run();
103     algorithmsScript = bar;
104   }
105 
106 }