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.multipole; 39 40 import static org.apache.commons.math3.util.FastMath.exp; 41 42 /** 43 * The TholeTensorQI class computes derivatives of Thole damping via recursion to order <= 4 for 44 * Cartesian multipoles in a quasi-internal frame. 45 * 46 * @author Michael J. Schnieders 47 * @see <a href="http://doi.org/10.1142/9789812830364_0002" target="_blank"> Matt Challacombe, Eric 48 * Schwegler and Jan Almlof, Modern developments in Hartree-Fock theory: Fast methods for 49 * computing the Coulomb matrix. Computational Chemistry: Review of Current Trends. pp. 53-107, 50 * Ed. J. Leczszynski, World Scientifc, 1996. </a> 51 * @since 1.0 52 */ 53 public class TholeTensorQI extends CoulombTensorQI { 54 55 /** Constant <code>threeFifths=3.0 / 5.0</code> */ 56 private static final double threeFifths = 3.0 / 5.0; 57 58 /** Constant <code>oneThirtyFifth=1.0 / 35.0</code> */ 59 private static final double oneThirtyFifth = 1.0 / 35.0; 60 61 /** 62 * Thole damping parameter is set to min(pti,ptk)). 63 */ 64 private double thole; 65 66 /** 67 * AiAk parameter = 1/(alphaI^6*alphaK^6) where alpha is polarizability. 68 */ 69 private double AiAk; 70 71 /** 72 * Constructor for TholeTensorQI. 73 * 74 * @param order Tensor order. 75 * @param thole Thole damping parameter is set to min(pti,ptk)). 76 * @param AiAk parameter = 1/(alphaI^6*alphaK^6) where alpha is polarizability. 77 */ 78 public TholeTensorQI(int order, double thole, double AiAk) { 79 super(order); 80 this.thole = thole; 81 this.AiAk = AiAk; 82 this.operator = OPERATOR.THOLE_FIELD; 83 84 assert (order <= 4); 85 } 86 87 /** 88 * Set Thole damping parameters 89 * 90 * @param thole a double. 91 * @param AiAk a double. 92 */ 93 public void setThole(double thole, double AiAk) { 94 this.thole = thole; 95 this.AiAk = AiAk; 96 } 97 98 /** 99 * Check if the Thole damping is exponential is greater than zero (or the interaction can be 100 * neglected). 101 * 102 * @param r The separation distance. 103 * @return True if -thole*u^3 is greater than -50.0. 104 */ 105 public boolean checkThole(double r) { 106 double rAiAk = r * AiAk; 107 return (-thole * rAiAk * rAiAk * rAiAk > -50.0); 108 } 109 110 /** 111 * Generate source terms for the Challacombe et al. recursion. 112 * 113 * @param T000 Location to store the source terms. 114 */ 115 protected void source(double[] T000) { 116 // Compute the normal Coulomb auxiliary term. 117 double ir = 1.0 / R; 118 double ir2 = ir * ir; 119 for (int n = 0; n < o1; n++) { 120 T000[n] = coulombSource[n] * ir; 121 ir *= ir2; 122 } 123 124 // Add the Thole damping terms: edamp = exp(-thole*u^3). 125 double u = R * AiAk; 126 double u3 = thole * u * u * u; 127 double u6 = u3 * u3; 128 double u9 = u6 * u3; 129 double expU3 = exp(-u3); 130 131 // The zeroth order term is not calculated for Thole damping. 132 T000[0] = 0.0; 133 T000[1] *= expU3; 134 T000[2] *= (1.0 + u3) * expU3; 135 T000[3] *= (1.0 + u3 + threeFifths * u6) * expU3; 136 T000[4] *= (1.0 + u3 + (18.0 * u6 + 9.0 * u9) * oneThirtyFifth) * expU3; 137 } 138 139 }