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.openmm.amoeba;
39
40 import ffx.openmm.Context;
41 import ffx.openmm.Force;
42 import ffx.openmm.IntArray;
43
44 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaVdwForce_addParticleType;
45 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaVdwForce_addParticle_1;
46 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaVdwForce_addTypePair;
47 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaVdwForce_create;
48 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaVdwForce_destroy;
49 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaVdwForce_setAlchemicalMethod;
50 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaVdwForce_setCutoffDistance;
51 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaVdwForce_setNonbondedMethod;
52 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaVdwForce_setParticleExclusions;
53 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaVdwForce_setParticleParameters;
54 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaVdwForce_setSoftcoreAlpha;
55 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaVdwForce_setSoftcorePower;
56 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaVdwForce_setUseDispersionCorrection;
57 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaVdwForce_updateParametersInContext;
58
59 /**
60 * Amoeba van der Waals Force.
61 */
62 public class VdwForce extends Force {
63
64 /**
65 * The Amoeba vdW Force constructor.
66 */
67 public VdwForce() {
68 pointer = OpenMM_AmoebaVdwForce_create();
69 }
70
71 /**
72 * Add a particle type to the vdW Force.
73 *
74 * @param rad The radius.
75 * @param eps The well depth.
76 * @return The type.
77 */
78 public int addParticleType(double rad, double eps) {
79 return OpenMM_AmoebaVdwForce_addParticleType(pointer, rad, eps);
80 }
81
82 /**
83 * Add a type pair to the vdW Force.
84 *
85 * @param type1 The first type.
86 * @param type2 The second type.
87 * @param rad The radius.
88 * @param eps The well depth.
89 */
90 public void addTypePair(int type1, int type2, double rad, double eps) {
91 OpenMM_AmoebaVdwForce_addTypePair(pointer, type1, type2, rad, eps);
92 }
93
94 /**
95 * Add a particle to the vdW Force.
96 *
97 * @param ired The particle ired.
98 * @param type The particle type.
99 * @param reductionFactor The reduction factor.
100 * @param isAlchemical The alchemical flag.
101 * @param scaleFactor The scale factor.
102 */
103 public void addParticle_1(int ired, int type, double reductionFactor, int isAlchemical, double scaleFactor) {
104 OpenMM_AmoebaVdwForce_addParticle_1(pointer, ired, type, reductionFactor, isAlchemical, scaleFactor);
105 }
106
107 /**
108 * Set the particle parameters.
109 *
110 * @param index The particle index.
111 * @param ired The particle reduction index.
112 * @param rad The radius.
113 * @param eps The well depth.
114 * @param reductionFactor The reduction factor.
115 * @param isAlchemical The alchemical flag.
116 * @param type The type.
117 * @param scaleFactor The scale factor.
118 */
119 public void setParticleParameters(int index, int ired, double rad, double eps, double reductionFactor,
120 int isAlchemical, int type, double scaleFactor) {
121 OpenMM_AmoebaVdwForce_setParticleParameters(pointer, index, ired, rad, eps, reductionFactor, isAlchemical, type, scaleFactor);
122 }
123
124 /**
125 * Set the cutoff distance.
126 *
127 * @param cutoff The cutoff distance.
128 */
129 public void setCutoffDistance(double cutoff) {
130 OpenMM_AmoebaVdwForce_setCutoffDistance(pointer, cutoff);
131 }
132
133 /**
134 * Set the vdW force to use a long-range dispersion correction.
135 *
136 * @param value The flag.
137 */
138 public void setUseDispersionCorrection(int value) {
139 OpenMM_AmoebaVdwForce_setUseDispersionCorrection(pointer, value);
140 }
141
142 /**
143 * Set the non-bonded method.
144 *
145 * @param method The non-bonded method.
146 */
147 public void setNonbondedMethod(int method) {
148 OpenMM_AmoebaVdwForce_setNonbondedMethod(pointer, method);
149 }
150
151 /**
152 * Set the alchemical method.
153 *
154 * @param method The alchemical method.
155 */
156 public void setAlchemicalMethod(int method) {
157 OpenMM_AmoebaVdwForce_setAlchemicalMethod(pointer, method);
158 }
159
160 /**
161 * Set the softcore power.
162 *
163 * @param vdWSoftcoreAlpha The softcore power.
164 */
165 public void setSoftcoreAlpha(double vdWSoftcoreAlpha) {
166 OpenMM_AmoebaVdwForce_setSoftcoreAlpha(pointer, vdWSoftcoreAlpha);
167 }
168
169 /**
170 * Set the softcore power.
171 *
172 * @param vdwSoftcorePower The softcore power.
173 */
174 public void setSoftcorePower(int vdwSoftcorePower) {
175 OpenMM_AmoebaVdwForce_setSoftcorePower(pointer, vdwSoftcorePower);
176 }
177
178 /**
179 * Set the particle exclusions.
180 *
181 * @param i The particle index.
182 * @param exclusions The exclusions.
183 */
184 public void setParticleExclusions(int i, IntArray exclusions) {
185 OpenMM_AmoebaVdwForce_setParticleExclusions(pointer, i, exclusions.getPointer());
186 }
187
188 /**
189 * Update the parameters in the OpenMM Context.
190 *
191 * @param context The OpenMM Context.
192 */
193 public void updateParametersInContext(Context context) {
194 if (context.hasContextPointer()) {
195 OpenMM_AmoebaVdwForce_updateParametersInContext(pointer, context.getPointer());
196 }
197 }
198
199 /**
200 * Destroy the vdW Force.
201 */
202 public void destroy() {
203 if (pointer != null) {
204 OpenMM_AmoebaVdwForce_destroy(pointer);
205 pointer = null;
206 }
207 }
208
209 }