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.potential.nonbonded.octree;
39
40 import java.util.logging.Logger;
41
42 /**
43 * OctreePoint: Object class for Octree method presented in the Fast Multipole Method (FMM) tutorial
44 * from the Barba Group: https://github.com/barbagroup/FMM_tutorial
45 */
46 public class OctreePoint {
47
48 private static final Logger logger = Logger.getLogger(OctreePoint.class.getName());
49
50 /** Coordinates of the point */
51 private double x;
52
53 private double y;
54 private double z;
55
56 /** Maximum value for random point coordinate Default = 1.0 */
57 private double domain = 1.0;
58
59 public OctreePoint(double[] coords, double domain) {
60
61 // Set max for random point coordinate generation
62 setDomain(domain);
63
64 // Assign input coordinates, if they are given
65 // Otherwise, assign random coordinates between 0 and domain
66 if (coords.length > 0) {
67 if (coords.length == 3) {
68 this.x = coords[0];
69 this.y = coords[1];
70 this.z = coords[2];
71 } else {
72 logger.warning("Coordinate array must have three points");
73 }
74 } else {
75 this.x = this.domain * Math.random();
76 this.y = this.domain * Math.random();
77 this.z = this.domain * Math.random();
78 }
79 }
80
81 public double distance(OctreePoint other) {
82 return Math.sqrt(
83 Math.pow((this.x - other.x), 2)
84 + Math.pow((this.y - other.y), 2)
85 + Math.pow((this.z - other.z), 2));
86 }
87
88 public double distance(OctreeCell other) {
89 return Math.sqrt(
90 Math.pow((this.x - other.getX()), 2)
91 + Math.pow((this.y - other.getY()), 2)
92 + Math.pow((this.z - other.getZ()), 2));
93 }
94
95 public double getX() {
96 return this.x;
97 }
98
99 public double getY() {
100 return this.y;
101 }
102
103 public double getZ() {
104 return this.z;
105 }
106
107 public void setDomain(double domain) {
108 this.domain = domain;
109 }
110 }