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 }