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
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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 import static java.lang.Math.fma;
41
42 /**
43 * The PolarizableMultipole class defines a polarizable multipole.
44 *
45 * @author Michael J. Schnieders
46 * @since 1.0
47 */
48 public class PolarizableMultipole {
49
50 private static final double oneThird = 1.0 / 3.0;
51 private static final double twoThirds = 2.0 / 3.0;
52
53 /**
54 * Partial charge.
55 */
56 protected double q;
57 /**
58 * Dipole x-component.
59 */
60 protected double dx;
61 /**
62 * Dipole y-component.
63 */
64 protected double dy;
65 /**
66 * Dipole z-component.
67 */
68 protected double dz;
69 /**
70 * Quadrupole xx-component multiplied by 1/3.
71 */
72 protected double qxx;
73 /**
74 * Quadrupole yy-component multiplied by 1/3.
75 */
76 protected double qyy;
77 /**
78 * Quadrupole zz-component multiplied by 1/3.
79 */
80 protected double qzz;
81 /**
82 * Quadrupole xy-component multiplied by 2/3.
83 */
84 protected double qxy;
85 /**
86 * Quadrupole xz-component multiplied by 2/3.
87 */
88 protected double qxz;
89 /**
90 * Quadrupole xz-component multiplied by 2/3.
91 */
92 protected double qyz;
93
94 /**
95 * Array of permanent multipole moments.
96 */
97 private final double[] M = new double[10];
98
99 /**
100 * Induced dipole x-component.
101 */
102 protected double ux;
103 /**
104 * Induced dipole y-component.
105 */
106 protected double uy;
107 /**
108 * Induced dipole z-component.
109 */
110 protected double uz;
111 /**
112 * Induced dipole chain rule x-component.
113 */
114 protected double px;
115 /**
116 * Induced dipole chain rule y-component.
117 */
118 protected double py;
119 /**
120 * Induced dipole chain rule z-component.
121 */
122 protected double pz;
123 /**
124 * Averaged induced dipole + induced dipole chain-rule x-component: sx = 0.5 * (ux + px).
125 */
126 protected double sx;
127 /**
128 * Averaged induced dipole + induced dipole chain-rule y-component: sy = 0.5 * (uy + py).
129 */
130 protected double sy;
131 /**
132 * Averaged induced dipole + induced dipole chain-rule z-component: sz = 0.5 * (uz + pz).
133 */
134 protected double sz;
135
136 /**
137 * PolarizableMultipole constructor with zero moments.
138 */
139 public PolarizableMultipole() {
140 }
141
142 /**
143 * PolarizableMultipole constructor.
144 *
145 * @param Q Multipole Q[q, dx, dy, dz, qxx, qyy, qzz, qxy, qxz, qyz]
146 * @param u Induced dipole u[ux, uy, uz]
147 * @param uCR Induced dipole chain-rule uCR[ux, uy, uz]
148 */
149 public PolarizableMultipole(double[] Q, double[] u, double[] uCR) {
150 setPermanentMultipole(Q);
151 setInducedDipole(u, uCR);
152 }
153
154 /**
155 * Set the permanent multipole.
156 * <p>
157 * Note that the quadrupole trace components are multiplied by 1/3 and the
158 * off-diagonal components are multiplied by 2/3.
159 *
160 * @param Q Multipole Q[q, dx, dy, dz, qxx, qyy, qzz, qxy, qxz, qyz]
161 * @param u Induced dipole u[ux, uy, uz]
162 * @param uCR Induced dipole chain-rule uCR[ux, uy, uz]
163 */
164 public void set(double[] Q, double[] u, double[] uCR) {
165 setPermanentMultipole(Q);
166 setInducedDipole(u, uCR);
167 }
168
169 /**
170 * Set the permanent multipole.
171 * <p>
172 * Note that the quadrupole trace components are multiplied by 1/3 and the
173 * off-diagonal components are multiplied by 2/3.
174 *
175 * @param Q Multipole Q[q, dx, dy, dz, qxx, qyy, qzz, qxy, qxz, qyz]
176 */
177 public final void setPermanentMultipole(double[] Q) {
178 q = Q[0];
179 dx = Q[1];
180 dy = Q[2];
181 dz = Q[3];
182 qxx = Q[4] * oneThird;
183 qyy = Q[5] * oneThird;
184 qzz = Q[6] * oneThird;
185 qxy = Q[7] * twoThirds;
186 qxz = Q[8] * twoThirds;
187 qyz = Q[9] * twoThirds;
188
189 M[0] = q;
190 M[1] = dx;
191 M[2] = dy;
192 M[3] = dz;
193 M[4] = qxx;
194 M[5] = qyy;
195 M[6] = qzz;
196 M[7] = qxy;
197 M[8] = qxz;
198 M[9] = qyz;
199 }
200
201 /**
202 * Set the induced dipole.
203 *
204 * @param u Induced dipole u[ux, uy, uz]
205 * @param uCR Induced dipole chain-rule uCR[ux, uy, uz]
206 */
207 public final void setInducedDipole(double[] u, double[] uCR) {
208 ux = u[0];
209 uy = u[1];
210 uz = u[2];
211 px = uCR[0];
212 py = uCR[1];
213 pz = uCR[2];
214 sx = 0.5 * (ux + px);
215 sy = 0.5 * (uy + py);
216 sz = 0.5 * (uz + pz);
217 }
218
219 /**
220 * Clear the induced dipoles.
221 */
222 public void clearInducedDipoles() {
223 ux = 0.0;
224 uy = 0.0;
225 uz = 0.0;
226 px = 0.0;
227 py = 0.0;
228 pz = 0.0;
229 sx = 0.0;
230 sy = 0.0;
231 sz = 0.0;
232 }
233
234 /**
235 * Compute the scaled and averaged induced dipole.
236 *
237 * @param scaleInduction Induction mask scale factor.
238 * @param scaleEnergy Energy mask scale factor.
239 */
240 public final void applyMasks(double scaleInduction, double scaleEnergy) {
241 // [Ux, Uy, Uz] resulted from induction masking rules, and we now apply the energy mask.
242 // [Px, Py, Pz] resulted from energy masking rules, and we now apply the induction mask.
243 sx = 0.5 * (ux * scaleEnergy + px * scaleInduction);
244 sy = 0.5 * (uy * scaleEnergy + py * scaleInduction);
245 sz = 0.5 * (uz * scaleEnergy + pz * scaleInduction);
246 }
247
248 /**
249 * Contract this multipole with the potential and its derivatives.
250 *
251 * @return The permanent multipole energy.
252 */
253 protected final double multipoleEnergy(double[] field) {
254 double total = 0.0;
255 for (int i = 0; i < 10; i++) {
256 total = fma(M[i], field[i], total);
257 }
258 return total;
259 }
260 }