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.openmm; 39 40 import com.sun.jna.ptr.PointerByReference; 41 import edu.uiowa.jopenmm.OpenMM_Vec3; 42 43 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_System_addConstraint; 44 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_System_addForce; 45 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_System_addParticle; 46 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_System_create; 47 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_System_destroy; 48 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_System_getNumConstraints; 49 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_System_removeForce; 50 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_System_setDefaultPeriodicBoxVectors; 51 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_System_setParticleMass; 52 53 /** 54 * This class represents a molecular system. The definition of a System involves 55 * four elements: 56 * 57 * <ul> 58 * <li>The set of particles in the system</li> 59 * <li>The forces acting on them</li> 60 * <li>Pairs of particles whose separation should be constrained to a fixed value</li> 61 * <li>For periodic systems, the dimensions of the periodic box</li> 62 * </ul> 63 * 64 * The particles and constraints are defined directly by the System object, while 65 * forces are defined by objects that extend the Force class. After creating a 66 * System, call addParticle() once for each particle, addConstraint() for each constraint, 67 * and addForce() for each Force. 68 * 69 * In addition, particles may be designated as "virtual sites". These are particles 70 * whose positions are computed automatically based on the positions of other particles. 71 * To define a virtual site, call setVirtualSite(), passing in a VirtualSite object 72 * that defines the rules for computing its position. 73 */ 74 public class System { 75 76 /** 77 * Context pointer. 78 */ 79 PointerByReference pointer; 80 81 /** 82 * Constructor. 83 */ 84 public System() { 85 pointer = OpenMM_System_create(); 86 } 87 88 /** 89 * Add a constraint to the system. 90 * 91 * @param particle1 The first particle. 92 * @param particle2 The second particle. 93 * @param distance The distance between the particles. 94 */ 95 public void addConstraint(int particle1, int particle2, double distance) { 96 OpenMM_System_addConstraint(pointer, particle1, particle2, distance); 97 } 98 99 /** 100 * Add a force to the system. 101 * 102 * @param force The force to add. 103 */ 104 public void addForce(Force force) { 105 if (force != null) { 106 int forceIndex = OpenMM_System_addForce(pointer, force.getPointer()); 107 force.setForceIndex(forceIndex); 108 } 109 } 110 111 /** 112 * Add a particle to the system. 113 * 114 * @param mass The mass of the particle. 115 */ 116 public void addParticle(double mass) { 117 OpenMM_System_addParticle(pointer, mass); 118 } 119 120 /** 121 * Get the number of constraints in the system. 122 * 123 * @return The number of constraints in the system. 124 */ 125 public int getNumConstraints() { 126 return OpenMM_System_getNumConstraints(pointer); 127 } 128 129 /** 130 * Remove a force from the system. 131 * 132 * @param index The index of the force to remove. 133 */ 134 public void removeForce(int index) { 135 OpenMM_System_removeForce(pointer, index); 136 } 137 138 /** 139 * Set the default periodic box vectors. 140 * 141 * @param a The first vector. 142 * @param b The second vector. 143 * @param c The third vector. 144 */ 145 public void setDefaultPeriodicBoxVectors(OpenMM_Vec3 a, OpenMM_Vec3 b, OpenMM_Vec3 c) { 146 OpenMM_System_setDefaultPeriodicBoxVectors(pointer, a, b, c); 147 } 148 149 150 /** 151 * Set the mass of a particle. 152 * 153 * @param index The index of the particle. 154 * @param mass The mass of the particle. 155 */ 156 public void setParticleMass(int index, double mass) { 157 OpenMM_System_setParticleMass(pointer, index, mass); 158 } 159 160 /** 161 * Get the pointer to the system. 162 * 163 * @return The pointer to the system. 164 */ 165 public PointerByReference getPointer() { 166 return pointer; 167 } 168 169 /** 170 * Destroy the system. 171 */ 172 public void destroy() { 173 if (pointer != null) { 174 OpenMM_System_destroy(pointer); 175 pointer = null; 176 } 177 } 178 179 }