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.numerics.multipole;
39
40 /**
41 * The PolarizableMultipole class defines a polarizable multipole.
42 *
43 * @author Michael J. Schnieders
44 * @since 1.0
45 */
46 public class PolarizableMultipole {
47
48 private static final double oneThird = 1.0 / 3.0;
49 private static final double twoThirds = 2.0 / 3.0;
50
51 /**
52 * Partial charge.
53 */
54 protected double q;
55 /**
56 * Dipole x-component.
57 */
58 protected double dx;
59 /**
60 * Dipole y-component.
61 */
62 protected double dy;
63 /**
64 * Dipole z-component.
65 */
66 protected double dz;
67 /**
68 * Quadrupole xx-component multiplied by 1/3.
69 */
70 protected double qxx;
71 /**
72 * Quadrupole yy-component multiplied by 1/3.
73 */
74 protected double qyy;
75 /**
76 * Quadrupole zz-component multiplied by 1/3.
77 */
78 protected double qzz;
79 /**
80 * Quadrupole xy-component multiplied by 2/3.
81 */
82 protected double qxy;
83 /**
84 * Quadrupole xz-component multiplied by 2/3.
85 */
86 protected double qxz;
87 /**
88 * Quadrupole xz-component multiplied by 2/3.
89 */
90 protected double qyz;
91
92 /**
93 * Induced dipole x-component.
94 */
95 protected double ux;
96 /**
97 * Induced dipole y-component.
98 */
99 protected double uy;
100 /**
101 * Induced dipole z-component.
102 */
103 protected double uz;
104 /**
105 * Induced dipole chain rule x-component.
106 */
107 protected double px;
108 /**
109 * Induced dipole chain rule y-component.
110 */
111 protected double py;
112 /**
113 * Induced dipole chain rule z-component.
114 */
115 protected double pz;
116 /**
117 * Averaged induced dipole + induced dipole chain-rule x-component: sx = 0.5 * (ux + px).
118 */
119 protected double sx;
120 /**
121 * Averaged induced dipole + induced dipole chain-rule y-component: sy = 0.5 * (uy + py).
122 */
123 protected double sy;
124 /**
125 * Averaged induced dipole + induced dipole chain-rule z-component: sz = 0.5 * (uz + pz).
126 */
127 protected double sz;
128 protected double Z;
129
130
131 /**
132 * PolarizableMultipole constructor with zero moments.
133 */
134 public PolarizableMultipole() {
135 }
136
137 /**
138 * PolarizableMultipole constructor.
139 *
140 * @param Q Multipole Q[q, dx, dy, dz, qxx, qyy, qzz, qxy, qxz, qyz]
141 * @param u Induced dipole u[ux, uy, uz]
142 * @param uCR Induced dipole chain-rule uCR[ux, uy, uz]
143 */
144 public PolarizableMultipole(double[] Q, double[] u, double[] uCR) {
145 setPermanentMultipole(Q);
146 setInducedDipole(u, uCR);
147 }
148
149 /**
150 * PolarizableMultipole constructor.
151 *
152 * @param Q Multipole Q[q, dx, dy, dz, qxx, qyy, qzz, qxy, qxz, qyz]
153 * @param u Induced dipole u[ux, uy, uz]
154 * @param uCR Induced dipole chain-rule uCR[ux, uy, uz]
155 */
156 public PolarizableMultipole(double[] Q, double[] u, double[] uCR, double Z) {
157 setPermanentMultipole(Q);
158 setInducedDipole(u, uCR);
159 this.Z = Z;
160 this.q = -Z + q;
161 }
162
163 /**
164 * Set the permanent multipole.
165 * <p>
166 * Note that the quadrupole trace components are multiplied by 1/3 and the
167 * off-diagonal components are multiplied by 2/3.
168 *
169 * @param Q Multipole Q[q, dx, dy, dz, qxx, qyy, qzz, qxy, qxz, qyz]
170 * @param u Induced dipole u[ux, uy, uz]
171 * @param uCR Induced dipole chain-rule uCR[ux, uy, uz]
172 */
173 public void set(double[] Q, double[] u, double[] uCR) {
174 setPermanentMultipole(Q);
175 setInducedDipole(u, uCR);
176 }
177
178 /**
179 * Set the permanent multipole.
180 * <p>
181 * Note that the quadrupole trace components are multiplied by 1/3 and the
182 * off-diagonal components are multiplied by 2/3.
183 *
184 * @param Q Multipole Q[q, dx, dy, dz, qxx, qyy, qzz, qxy, qxz, qyz]
185 */
186 public final void setPermanentMultipole(double[] Q) {
187 q = Q[0];
188 dx = Q[1];
189 dy = Q[2];
190 dz = Q[3];
191 qxx = Q[4] * oneThird;
192 qyy = Q[5] * oneThird;
193 qzz = Q[6] * oneThird;
194 qxy = Q[7] * twoThirds;
195 qxz = Q[8] * twoThirds;
196 qyz = Q[9] * twoThirds;
197 }
198
199 /**
200 * Set the induced dipole.
201 *
202 * @param u Induced dipole u[ux, uy, uz]
203 * @param uCR Induced dipole chain-rule uCR[ux, uy, uz]
204 */
205 public final void setInducedDipole(double[] u, double[] uCR) {
206 ux = u[0];
207 uy = u[1];
208 uz = u[2];
209 px = uCR[0];
210 py = uCR[1];
211 pz = uCR[2];
212 sx = 0.5 * (ux + px);
213 sy = 0.5 * (uy + py);
214 sz = 0.5 * (uz + pz);
215 }
216
217 /**
218 * Clear the induced dipoles.
219 */
220 public void clearInducedDipoles() {
221 ux = 0.0;
222 uy = 0.0;
223 uz = 0.0;
224 px = 0.0;
225 py = 0.0;
226 pz = 0.0;
227 sx = 0.0;
228 sy = 0.0;
229 sz = 0.0;
230 }
231
232 /**
233 * Compute the scaled and averaged induced dipole.
234 *
235 * @param scaleInduction Induction mask scale factor.
236 * @param scaleEnergy Energy mask scale factor.
237 */
238 public final void applyMasks(double scaleInduction, double scaleEnergy) {
239 // [Ux, Uy, Uz] resulted from induction masking rules, and we now apply the energy mask.
240 // [Px, Py, Pz] resulted from energy masking rules, and we now apply the induction mask.
241 sx = 0.5 * (ux * scaleEnergy + px * scaleInduction);
242 sy = 0.5 * (uy * scaleEnergy + py * scaleInduction);
243 sz = 0.5 * (uz * scaleEnergy + pz * scaleInduction);
244 }
245
246 }