1 | /*
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2 | * Project: MoleCuilder
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3 | * Description: creates and alters molecular systems
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4 | * Copyright (C) 2012 University of Bonn. All rights reserved.
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5 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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6 | */
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7 |
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8 | /*
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9 | * LinkedCell_View.cpp
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10 | *
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11 | * Created on: Nov 15, 2011
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12 | * Author: heber
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13 | */
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14 |
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15 | // include config.h
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16 | #ifdef HAVE_CONFIG_H
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17 | #include <config.h>
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18 | #endif
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19 |
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20 | #include "CodePatterns/MemDebug.hpp"
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21 |
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22 | #include "LinkedCell_View.hpp"
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23 |
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24 | #include <algorithm>
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25 |
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26 | #include "CodePatterns/Assert.hpp"
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27 | #include "CodePatterns/Log.hpp"
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28 |
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29 | #include "Atom/TesselPoint.hpp"
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30 | #include "Box.hpp"
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31 | #include "LinearAlgebra/Vector.hpp"
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32 | #include "LinkedCell.hpp"
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33 | #include "LinkedCell_Model.hpp"
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34 | #include "LinkedCell_View_ModelWrapper.hpp"
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35 | #include "tripleIndex.hpp"
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36 |
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37 | using namespace LinkedCell;
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38 |
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39 | // static multimap instance
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40 | LinkedCell_View::ModelInstanceMap LinkedCell_View::RAIIMap;
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41 |
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42 | /** Constructor of class LinkedCell_View.
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43 | *
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44 | * We add ourselves to RAIIMap here.
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45 | */
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46 | LinkedCell_View::LinkedCell_View(const LinkedCell_Model &_LC) :
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47 | LC( new LinkedCell_View_ModelWrapper(&_LC) )
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48 | {
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49 | // add us to RAII counting map
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50 | #ifndef NDEBUG
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51 | std::pair< ModelInstanceMap::iterator, bool> inserter =
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52 | #endif
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53 | RAIIMap.insert( this );
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54 | ASSERT( inserter.second,
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55 | "LinkedCell_View::LinkedCell_View() - we "+toString(this)+" are already present in RAIIMap.");
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56 | LOG(3, "INFO: Placing instance "+toString(this)+" into RAIIMap.");
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57 | }
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58 |
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59 | /** Copy Constructor of class LinkedCell_View.
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60 | *
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61 | * We add ourselves to RAIIMap here.
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62 | */
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63 | LinkedCell_View::LinkedCell_View(const LinkedCell_View &_view) :
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64 | LC( new LinkedCell_View_ModelWrapper(_view.LC->getModel()) )
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65 | {
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66 | if (this != &_view) {
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67 | // add us to RAII counting map
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68 | #ifndef NDEBUG
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69 | std::pair< ModelInstanceMap::iterator, bool> inserter =
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70 | #endif
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71 | RAIIMap.insert( this );
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72 | ASSERT( inserter.second,
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73 | "LinkedCell_View::LinkedCell_View(&view) - we "+toString(this)+" are already present in RAIIMap.");
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74 | LOG(3, "INFO: Placing instance "+toString(this)+" copied from "+toString(&_view)+" into RAIIMap.");
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75 | }
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76 | }
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77 |
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78 | /** Destructor of class LinkedCell_View.
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79 | *
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80 | * We remove ourselves from RAIIMap here.
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81 | */
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82 | LinkedCell_View::~LinkedCell_View()
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83 | {
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84 | ModelInstanceMap::iterator iter = RAIIMap.find(this);
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85 | ASSERT( iter != RAIIMap.end(),
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86 | "LinkedCell_View::~LinkedCell_View() - there is no instance "
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87 | +toString(this)+" in RAIIMap.");
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88 | if (iter != RAIIMap.end()) {
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89 | RAIIMap.erase(iter);
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90 | LOG(3, "INFO: Removing instance "+toString(this)+" from RAIIMap.");
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91 | } else {
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92 | ELOG(1, "Failed to remove instance "+toString(this)+" from RAIIMap.");
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93 | }
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94 | delete LC;
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95 | }
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96 |
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97 | /** Return at least as many points as are inside a sphere of \a radius around \a center.
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98 | *
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99 | * \sa LinkedCell_View::getPointsInsideSphere()
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100 | *
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101 | * @param radius radius of sphere
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102 | * @param center center of sphere
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103 | * @return a list containing at least all points inside described sphere
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104 | */
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105 | LinkedList LinkedCell_View::getAllNeighbors(const double radius, const Vector ¢er) const
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106 | {
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107 | LinkedList TesselList; // we do not need a set, as nodes are uniquely associated to a cell.
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108 |
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109 | const LinkedCell_Model * const LCmodel = LC->getModel(); // get quick ref to model
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110 | // get relative bounds
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111 | const tripleIndex step = LCmodel->getStep(radius);
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112 | const tripleIndex index = LCmodel->getIndexToVector(center);
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113 | LinkedCell_Model::LinkedCellNeighborhoodBounds neighbors =
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114 | LCmodel->getNeighborhoodBounds(index, step);
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115 |
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116 | tripleIndex n;
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117 | for (n[0] = 0; n[0] < neighbors.second[0]; n[0]++)
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118 | for (n[1] = 0; n[1] < neighbors.second[1]; n[1]++)
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119 | for (n[2] = 0; n[2] < neighbors.second[2]; n[2]++) {
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120 | tripleIndex absolute_n = neighbors.first + n;
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121 | if (!LCmodel->checkArrayBounds(absolute_n))
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122 | LCmodel->applyBoundaryConditions(absolute_n);
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123 | const LinkedCell &List = LCmodel->getCell(absolute_n);
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124 | LOG(3, "INFO: Current cell is " << neighbors.first << " plus " << n << ", yielding " << absolute_n << ".");
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125 | for (LinkedCell::const_iterator Runner = List.begin(); Runner != List.end(); Runner++)
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126 | TesselList.insert(*Runner);
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127 | }
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128 | return TesselList;
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129 | }
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130 |
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131 | LinkedList LinkedCell_View::getPointsInsideSphere(const double radius, const Vector ¢er) const
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132 | {
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133 | // get overly much points
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134 | const LinkedList TesselList = getAllNeighbors(radius, center);
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135 | LinkedList ReturnList;
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136 |
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137 | // remove all unnecessary ones
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138 | const Box& domain = LC->getModel()->getDomain();
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139 | for (LinkedList::const_iterator iter = TesselList.begin(); iter != TesselList.end(); ++iter) {
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140 | if (domain.periodicDistanceSquared(center, (*iter)->getPosition()) <= radius*radius)
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141 | ReturnList.insert(*iter);
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142 | }
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143 |
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144 | return ReturnList;
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145 | }
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