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.numerics.integrate; 39 40 import static java.lang.String.format; 41 import static java.lang.System.arraycopy; 42 import static org.apache.commons.math3.util.FastMath.cos; 43 import static org.apache.commons.math3.util.FastMath.sin; 44 45 /** 46 * A CosineWave describes points along a sine wave of f(x) = a*sin(jx). 47 * 48 * @author Jacob M. Litman 49 */ 50 public class CosineWave extends FunctionDataCurve { 51 52 /** Magnitude. */ 53 private final double a; 54 /** Periodicity. */ 55 private final double n; 56 /** Inverse periodicity. */ 57 private final double nInverse; 58 59 /** 60 * Constructs f(x) = a*cos(nx). 61 * 62 * @param x an array of {@link double} objects. 63 * @param a the magnitude. 64 * @param n the periodicity. 65 */ 66 public CosineWave(double[] x, double a, double n) { 67 this(x, false, a, n); 68 } 69 70 /** 71 * Constructs f(x) = a*cos(nx). 72 * 73 * @param x an array of {@link double} objects. 74 * @param halfWidthEnds Use half-width start and end bins. 75 * @param a the magnitude. 76 * @param n the periodicity. 77 */ 78 public CosineWave(double[] x, boolean halfWidthEnds, double a, double n) { 79 int nPoints = x.length; 80 points = new double[nPoints]; 81 this.a = a; 82 this.n = n; 83 nInverse = 1.0 / n; 84 this.halfWidthEnd = halfWidthEnds; 85 86 for (int i = 0; i < points.length; i++) { 87 points[i] = cosAt(x[i]); 88 } 89 lb = x[0]; 90 ub = x[nPoints - 1]; 91 this.x = new double[x.length]; 92 arraycopy(x, 0, this.x, 0, x.length); 93 } 94 95 /** {@inheritDoc} */ 96 @Override 97 public double fX(double x) { 98 return cosAt(x); 99 } 100 101 /** {@inheritDoc} */ 102 @Override 103 public double integralAt(double x) { 104 return a * nInverse * sin(n * x); 105 } 106 107 /** {@inheritDoc} */ 108 @Override 109 public String toString() { 110 StringBuilder sb = new StringBuilder("Cosine wave f(x) = "); 111 sb.append(a).append("*cos(").append(n).append("x)"); 112 sb.append( 113 format( 114 " with %d points from lower bound %9.3g and upper bound %9.3g", points.length, lb, ub)); 115 if (halfWidthEnd) { 116 sb.append(" and half-width start/end bins"); 117 } 118 119 return sb.toString(); 120 } 121 122 // Private, non-overrideable method for use in the constructor. 123 private double cosAt(double x) { 124 return a * cos(n * x); 125 } 126 }