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.xray.scatter;
39
40 import ffx.xray.refine.RefinementMode;
41
42 import static org.apache.commons.math3.util.FastMath.PI;
43 import static org.apache.commons.math3.util.FastMath.pow;
44
45 /**
46 * FormFactor interface.
47 *
48 * @author Timothy D. Fenn
49 * @since 1.0
50 */
51 public interface FormFactor {
52
53 /**
54 * Compute the real space density rho
55 *
56 * @param f the current density to modify
57 * @param lambda the state variable
58 * @param xyz the requested point for evaluating density
59 * @return the real space density value at xyz
60 */
61 double rho(double f, double lambda, double[] xyz);
62
63 /**
64 * Compute the real space gradient
65 *
66 * @param xyz the requested point for evaluating gradient
67 * @param dfc the multiplier to apply to the gradient
68 * @param refinementmode {@link RefinementMode} determines which
69 * gradients will be computed
70 */
71 void rhoGrad(double[] xyz, double dfc, RefinementMode refinementmode);
72
73 /**
74 * update the coordinates to the current position
75 *
76 * @param xyz an array of double.
77 */
78 void update(double[] xyz);
79
80 /**
81 * update the coordinates to the current position and Badd
82 *
83 * @param xyz an array of double.
84 * @param badd a double.
85 */
86 void update(double[] xyz, double badd);
87
88 double[] v0 = {0.0, 0.0, 0.0};
89 double[] vx = {1.0, 0.0, 0.0};
90 double[] vy = {0.0, 1.0, 0.0};
91 double[] vz = {0.0, 0.0, 1.0};
92 double[][] dUdU11 = {vx, v0, v0};
93 double[][] dUdU22 = {v0, vy, v0};
94 double[][] dUdU33 = {v0, v0, vz};
95 double[][] dUdU12 = {vy, vx, v0};
96 double[][] dUdU13 = {vz, v0, vx};
97 double[][] dUdU23 = {v0, vz, vy};
98 double twoPI2 = 2.0 * PI * PI;
99 double inverseTwoPI32 = pow(2.0 * PI, -1.5);
100 double oneThird = 1.0 / 3.0;
101 }