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.xray;
39
40 import static ffx.numerics.math.DoubleMath.length2;
41 import static ffx.numerics.math.DoubleMath.sub;
42 import static org.apache.commons.math3.util.FastMath.exp;
43
44 import ffx.potential.bonded.Atom;
45 import ffx.xray.RefinementMinimize.RefinementMode;
46
47 /**
48 * SolventGaussFormFactor class.
49 *
50 * @author Timothy D. Fenn
51 * @since 1.0
52 */
53 public final class SolventGaussFormFactor implements FormFactor {
54
55 private final Atom atom;
56 private final double[] xyz = new double[3];
57 private final double[] dxyz = new double[3];
58 private final double[] g = new double[3];
59 private final double isd2;
60
61 /**
62 * Constructor for SolventGaussFormFactor.
63 *
64 * @param atom a {@link ffx.potential.bonded.Atom} object.
65 * @param sd a double.
66 */
67 public SolventGaussFormFactor(Atom atom, double sd) {
68 this(atom, sd, atom.getXYZ(null));
69 }
70
71 /**
72 * Constructor for SolventGaussFormFactor.
73 *
74 * @param atom a {@link ffx.potential.bonded.Atom} object.
75 * @param sd a double.
76 * @param xyz an array of double.
77 */
78 public SolventGaussFormFactor(Atom atom, double sd, double[] xyz) {
79 this.atom = atom;
80 isd2 = 1.0 / (sd * sd);
81 update(xyz);
82 }
83
84 /** {@inheritDoc} */
85 @Override
86 public double rho(double f, double lambda, double[] xyz) {
87 sub(this.xyz, xyz, dxyz);
88 return rho(f, lambda, length2(dxyz));
89 }
90
91 /**
92 * rho
93 *
94 * @param f a double.
95 * @param lambda a double.
96 * @param rsq a double.
97 * @return a double.
98 */
99 public double rho(double f, double lambda, double rsq) {
100 return f + exp(-rsq * isd2);
101 }
102
103 /** {@inheritDoc} */
104 @Override
105 public void rhoGrad(double[] xyz, double dfc, RefinementMode refinementmode) {
106 if (refinementmode == RefinementMode.BFACTORS
107 || refinementmode == RefinementMode.OCCUPANCIES
108 || refinementmode == RefinementMode.BFACTORS_AND_OCCUPANCIES) {
109 return;
110 }
111 sub(this.xyz, xyz, dxyz);
112 double r2 = length2(dxyz);
113 double rho = exp(-r2 * isd2);
114 double prefactor = -dfc * 2.0 * rho * isd2;
115 g[0] = prefactor * dxyz[0];
116 g[1] = prefactor * dxyz[1];
117 g[2] = prefactor * dxyz[2];
118 atom.addToXYZGradient(g[0], g[1], g[2]);
119 }
120
121 /** {@inheritDoc} */
122 @Override
123 public void update(double[] xyz) {
124 update(xyz, 0.0);
125 }
126
127 /** {@inheritDoc} */
128 @Override
129 public void update(double[] xyz, double badd) {
130 this.xyz[0] = xyz[0];
131 this.xyz[1] = xyz[1];
132 this.xyz[2] = xyz[2];
133 }
134 }