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.openmm;
39
40 import com.sun.jna.ptr.DoubleByReference;
41 import com.sun.jna.ptr.IntByReference;
42 import com.sun.jna.ptr.PointerByReference;
43
44 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Continuous3DFunction_create;
45 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Continuous3DFunction_destroy;
46 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Continuous3DFunction_getFunctionParameters;
47 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Continuous3DFunction_setFunctionParameters;
48
49 /**
50 * This is a TabulatedFunction that computes a continuous three dimensional function.
51 */
52 public class Continuous3DFunction extends TabulatedFunction {
53
54 /**
55 * Create a Continuous3DFunction f(x,y,z) based on a set of tabulated values.
56 *
57 * @param values the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
58 * and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax.
59 * A natural cubic spline is used to interpolate between the tabulated values. The function is
60 * assumed to be zero when x, y, or z is outside its specified range. The values should be ordered so
61 * that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x.
62 * This must be of length xsize*ysize*zsize.
63 * @param xsize the number of table elements along the x direction
64 * @param ysize the number of table elements along the y direction
65 * @param zsize the number of table elements along the z direction
66 * @param xmin the value of x corresponding to the first element of values
67 * @param xmax the value of x corresponding to the last element of values
68 * @param ymin the value of y corresponding to the first element of values
69 * @param ymax the value of y corresponding to the last element of values
70 * @param zmin the value of z corresponding to the first element of values
71 * @param zmax the value of z corresponding to the last element of values
72 * @param periodic whether the interpolated function is periodic
73 */
74 public Continuous3DFunction(PointerByReference values, int xsize, int ysize, int zsize, double xmin, double xmax,
75 double ymin, double ymax, double zmin, double zmax, boolean periodic) {
76 super(OpenMM_Continuous3DFunction_create(xsize, ysize, zsize, values, xmin, xmax, ymin, ymax, zmin, zmax, periodic ? 1 : 0));
77 }
78
79 /**
80 * Destroy the continuous 3D function.
81 */
82 @Override
83 public void destroy() {
84 if (pointer != null) {
85 OpenMM_Continuous3DFunction_destroy(pointer);
86 pointer = null;
87 }
88 }
89
90 /**
91 * Get the parameters for the tabulated function.
92 *
93 * @param values the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
94 * and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax.
95 * A natural cubic spline is used to interpolate between the tabulated values. The function is
96 * assumed to be zero when x, y, or z is outside its specified range. The values should be ordered so
97 * that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x.
98 * This must be of length xsize*ysize*zsize.
99 * @param xsize the number of table elements along the x direction
100 * @param ysize the number of table elements along the y direction
101 * @param zsize the number of table elements along the z direction
102 * @param xmin the value of x corresponding to the first element of values
103 * @param xmax the value of x corresponding to the last element of values
104 * @param ymin the value of y corresponding to the first element of values
105 * @param ymax the value of y corresponding to the last element of values
106 * @param zmin the value of z corresponding to the first element of values
107 * @param zmax the value of z corresponding to the last element of values
108 */
109 public void getFunctionParameters(PointerByReference values, IntByReference xsize, IntByReference ysize, IntByReference zsize,
110 DoubleByReference xmin, DoubleByReference xmax,
111 DoubleByReference ymin, DoubleByReference ymax,
112 DoubleByReference zmin, DoubleByReference zmax) {
113 OpenMM_Continuous3DFunction_getFunctionParameters(pointer, xsize, ysize, zsize, values, xmin, xmax, ymin, ymax, zmin, zmax);
114 }
115
116 /**
117 * Set the parameters for the tabulated function.
118 *
119 * @param values the tabulated values of the function f(x,y,z) at xsize uniformly spaced values of x between xmin
120 * and xmax, ysize values of y between ymin and ymax, and zsize values of z between zmin and zmax.
121 * A natural cubic spline is used to interpolate between the tabulated values. The function is
122 * assumed to be zero when x, y, or z is outside its specified range. The values should be ordered so
123 * that values[i+xsize*j+xsize*ysize*k] = f(x_i,y_j,z_k), where x_i is the i'th uniformly spaced value of x.
124 * This must be of length xsize*ysize*zsize.
125 * @param xsize the number of table elements along the x direction
126 * @param ysize the number of table elements along the y direction
127 * @param zsize the number of table elements along the z direction
128 * @param xmin the value of x corresponding to the first element of values
129 * @param xmax the value of x corresponding to the last element of values
130 * @param ymin the value of y corresponding to the first element of values
131 * @param ymax the value of y corresponding to the last element of values
132 * @param zmin the value of z corresponding to the first element of values
133 * @param zmax the value of z corresponding to the last element of values
134 */
135 public void setFunctionParameters(PointerByReference values, int xsize, int ysize, int zsize,
136 double xmin, double xmax, double ymin, double ymax,
137 double zmin, double zmax) {
138 OpenMM_Continuous3DFunction_setFunctionParameters(pointer, xsize, ysize, zsize, values, xmin, xmax, ymin, ymax, zmin, zmax);
139 }
140 }