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 BARFilesTest extends AlgorithmsTest {
46
47
48 /**
49 * Tests BAR script with tinker bar files input.
50 */
51 // @Test
52 public void testBARFiles() {
53
54 if (!ffxOpenMM) {
55 return;
56 }
57
58 // Set-up the input arguments for the script.
59 String filepath = getResourcePath("testBar/singleTopology/dimethylphosphate.100.xyz");
60 String[] args = {"-t", "298", "--nw", "8", "--ac", "1-13", "--utb", filepath};
61 binding.setVariable("args", args);
62 // Evaluate the script.
63 BAR bar = new BAR(binding).run();
64 algorithmsScript = bar;
65
66 FreeEnergyDifferenceReporter reporter = bar.getReporter();
67
68 double expectedFepFor = -115.4001;
69 double actualFepFor = reporter.getForwardTotalFEDifference();
70 Assert.assertEquals(expectedFepFor, actualFepFor, 0.5);
71
72 double expectedFepBack = -118.6607;
73 double actualFepBack = reporter.getBackwardTotalFEDifference();
74 Assert.assertEquals(expectedFepBack, actualFepBack, 0.5);
75
76 double expectedhFor = -157.1466;
77 double actualhFor = reporter.getForwardTotalEnthalpyChange();
78 Assert.assertEquals(expectedhFor, actualhFor, 50);
79
80 double expectedhBack = 123.5150;
81 double actualhBack = reporter.getBackwardTotalEnthalpyChange();
82 Assert.assertEquals(expectedhBack, actualhBack, 90);
83
84 double expectedhBAR = -29.0062;
85 double actualhBAR = reporter.getBarBSTotalEnthalpyChange();
86 Assert.assertEquals(expectedhBAR, actualhBAR, 4);
87
88 double expectedBARIteration = -117.1754;
89 double actualBARIteration = reporter.getBarIterTotalFEDiff();
90 Assert.assertEquals(expectedBARIteration, actualBARIteration, 0.5);
91
92 double expectedBARBootstrap = -117.1464;
93 double actualBARBootstrap = reporter.getBarBSTotalFEDiff();
94 Assert.assertEquals(expectedBARBootstrap, actualBARBootstrap, 0.3);
95 }
96
97 @Test
98 public void testBARHelp() {
99 String[] args = {"-h"};
100 binding.setVariable("args", args);
101
102 // Evaluate the script.
103 BAR bar = new BAR(binding).run();
104 algorithmsScript = bar;
105 }
106
107 }