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 BARDualTopologyTest 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 String hispath = getResourcePath("testBar/dualTopology/HIS_solv.20.xyz");
58 String hidpath = getResourcePath("testBar/dualTopology/HID_solv.20.xyz");
59
60 // Set-up the input arguments for the script.
61 String[] args = {"-t", "298", "--nw", "8", "--ac", "28", hispath, hidpath};
62 binding.setVariable("args", args);
63 // Evaluate the script.
64 BAR bar = new BAR(binding).run();
65 algorithmsScript = bar;
66
67 System.out.println("after run");
68
69 FreeEnergyDifferenceReporter reporter = bar.getReporter();
70
71 double expectedFepFor = -36.4647;
72 double actualFepFor = reporter.getForwardTotalFEDifference();
73 Assert.assertEquals(expectedFepFor, actualFepFor, 0.7);
74
75 double expectedFepBack = -36.0005;
76 double actualFepBack = reporter.getBackwardTotalFEDifference();
77 Assert.assertEquals(expectedFepBack, actualFepBack, 0.7);
78
79 double expectedhFor = -8.7772;
80 double actualhFor = reporter.getForwardTotalEnthalpyChange();
81 Assert.assertEquals(expectedhFor, actualhFor, 70);
82
83 double expectedhBack = 27.7404;
84 double actualhBack = reporter.getBackwardTotalEnthalpyChange();
85 Assert.assertEquals(expectedhBack, actualhBack, 60);
86
87 double expectedhBAR = 14.188;
88 double actualhBAR = reporter.getBarBSTotalEnthalpyChange();
89 Assert.assertEquals(expectedhBAR, actualhBAR, 7);
90
91 double expectedBARIteration = -35.7346;
92 double actualBARIteration = reporter.getBarIterTotalFEDiff();
93 Assert.assertEquals(expectedBARIteration, actualBARIteration, 1.0);
94
95 double expectedBARBootstrap = -35.9829;
96 double actualBARBootstrap = reporter.getBarBSTotalFEDiff();
97 Assert.assertEquals(expectedBARBootstrap, actualBARBootstrap, 1.0);
98 }
99
100 @Test
101 public void testBARHelp() {
102 String[] args = {"-h"};
103 binding.setVariable("args", args);
104
105 // Evaluate the script.
106 BAR bar = new BAR(binding).run();
107 algorithmsScript = bar;
108 }
109
110 }