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) 2010 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 | /** \file atom.cpp
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9 | *
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10 | * Function implementations for the class atom.
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11 | *
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12 | */
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13 |
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14 | // include config.h
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15 | #ifdef HAVE_CONFIG_H
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16 | #include <config.h>
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17 | #endif
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18 |
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19 | #include "CodePatterns/MemDebug.hpp"
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20 |
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21 | #include "atom.hpp"
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22 | #include "Bond/bond.hpp"
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23 | #include "CodePatterns/Log.hpp"
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24 | #include "config.hpp"
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25 | #include "element.hpp"
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26 | #include "parser.hpp"
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27 | #include "LinearAlgebra/Vector.hpp"
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28 | #include "World.hpp"
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29 | #include "molecule.hpp"
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30 | #include "Shapes/Shape.hpp"
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31 |
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32 | #include <iomanip>
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33 | #include <iostream>
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34 |
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35 | /************************************* Functions for class atom *************************************/
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36 |
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37 |
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38 | /** Constructor of class atom.
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39 | */
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40 | atom::atom() :
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41 | father(this),
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42 | sort(&Nr),
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43 | mol(0)
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44 | {};
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45 |
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46 | /** Constructor of class atom.
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47 | */
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48 | atom::atom(atom *pointer) :
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49 | ParticleInfo(pointer),
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50 | father(pointer),
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51 | sort(&Nr),
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52 | mol(0)
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53 | {
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54 | setType(pointer->getType()); // copy element of atom
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55 | AtomicPosition = pointer->AtomicPosition; // copy trajectory of coordination
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56 | AtomicVelocity = pointer->AtomicVelocity; // copy trajectory of velocity
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57 | AtomicForce = pointer->AtomicForce;
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58 | setFixedIon(pointer->getFixedIon());
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59 | };
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60 |
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61 | atom *atom::clone(){
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62 | atom *res = new atom(this);
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63 | World::getInstance().registerAtom(res);
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64 | return res;
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65 | }
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66 |
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67 |
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68 | /** Destructor of class atom.
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69 | */
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70 | atom::~atom()
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71 | {
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72 | removeFromMolecule();
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73 | };
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74 |
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75 |
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76 | void atom::UpdateSteps()
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77 | {
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78 | LOG(4,"atom::UpdateSteps() called.");
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79 | // append to position, velocity and force vector
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80 | AtomInfo::AppendTrajectoryStep();
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81 | // append to ListOfBonds vector
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82 | BondedParticleInfo::AppendTrajectoryStep();
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83 | }
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84 |
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85 | /** Climbs up the father list until NULL, last is returned.
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86 | * \return true father, i.e. whose father points to itself, NULL if it could not be found or has none (added hydrogen)
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87 | */
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88 | atom *atom::GetTrueFather()
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89 | {
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90 | if(father == this){ // top most father is the one that points on itself
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91 | return this;
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92 | }
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93 | else if(!father) {
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94 | return 0;
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95 | }
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96 | else {
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97 | return father->GetTrueFather();
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98 | }
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99 | };
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100 |
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101 | /** Sets father to itself or its father in case of copying a molecule.
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102 | */
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103 | void atom::CorrectFather()
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104 | {
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105 | if (father->father == father) // same atom in copy's father points to itself
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106 | father = this; // set father to itself (copy of a whole molecule)
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107 | else
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108 | father = father->father; // set father to original's father
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109 |
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110 | };
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111 |
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112 | /** Check whether father is equal to given atom.
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113 | * \param *ptr atom to compare father to
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114 | * \param **res return value (only set if atom::father is equal to \a *ptr)
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115 | */
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116 | void atom::EqualsFather ( const atom *ptr, const atom **res ) const
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117 | {
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118 | if ( ptr == father )
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119 | *res = this;
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120 | };
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121 |
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122 | bool atom::isFather(const atom *ptr){
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123 | return ptr==father;
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124 | }
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125 |
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126 | /** Checks whether atom is within the given box.
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127 | * \param offset offset to box origin
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128 | * \param *parallelepiped box matrix
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129 | * \return true - is inside, false - is not
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130 | */
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131 | bool atom::IsInShape(const Shape& shape) const
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132 | {
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133 | return shape.isInside(getPosition());
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134 | };
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135 |
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136 | /** Output of a single atom with given numbering.
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137 | * \param ElementNo cardinal number of the element
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138 | * \param AtomNo cardinal number among these atoms of the same element
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139 | * \param *out stream to output to
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140 | * \param *comment commentary after '#' sign
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141 | * \return true - \a *out present, false - \a *out is NULL
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142 | */
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143 | bool atom::OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment) const
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144 | {
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145 | if (out != NULL) {
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146 | *out << "Ion_Type" << ElementNo << "_" << AtomNo << "\t" << fixed << setprecision(9) << showpoint;
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147 | *out << at(0) << "\t" << at(1) << "\t" << at(2);
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148 | *out << "\t" << (int)(getFixedIon());
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149 | if (getAtomicVelocity().Norm() > MYEPSILON)
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150 | *out << "\t" << scientific << setprecision(6) << getAtomicVelocity()[0] << "\t" << getAtomicVelocity()[1] << "\t" << getAtomicVelocity()[2] << "\t";
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151 | if (comment != NULL)
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152 | *out << " # " << comment << endl;
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153 | else
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154 | *out << " # molecule nr " << getNr() << endl;
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155 | return true;
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156 | } else
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157 | return false;
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158 | };
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159 |
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160 | /** Output of a single atom with numbering from array according to atom::type.
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161 | * \param *ElementNo cardinal number of the element
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162 | * \param *AtomNo cardinal number among these atoms of the same element
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163 | * \param *out stream to output to
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164 | * \param *comment commentary after '#' sign
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165 | * \return true - \a *out present, false - \a *out is NULL
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166 | */
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167 | bool atom::OutputArrayIndexed(ostream * const out,const enumeration<const element*> &elementLookup, int *AtomNo, const char *comment) const
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168 | {
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169 | AtomNo[getType()->getAtomicNumber()]++; // increment number
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170 | if (out != NULL) {
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171 | const element *elemental = getType();
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172 | ASSERT(elementLookup.there.find(elemental)!=elementLookup.there.end(),"Type of this atom was not in the formula upon enumeration");
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173 | *out << "Ion_Type" << elementLookup.there.find(elemental)->second << "_" << AtomNo[elemental->getAtomicNumber()] << "\t" << fixed << setprecision(9) << showpoint;
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174 | *out << at(0) << "\t" << at(1) << "\t" << at(2);
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175 | *out << "\t" << getFixedIon();
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176 | if (getAtomicVelocity().Norm() > MYEPSILON)
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177 | *out << "\t" << scientific << setprecision(6) << getAtomicVelocity()[0] << "\t" << getAtomicVelocity()[1] << "\t" << getAtomicVelocity()[2] << "\t";
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178 | if (comment != NULL)
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179 | *out << " # " << comment << endl;
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180 | else
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181 | *out << " # molecule nr " << getNr() << endl;
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182 | return true;
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183 | } else
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184 | return false;
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185 | };
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186 |
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187 | /** Output of a single atom as one line in xyz file.
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188 | * \param *out stream to output to
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189 | * \return true - \a *out present, false - \a *out is NULL
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190 | */
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191 | bool atom::OutputXYZLine(ofstream *out) const
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192 | {
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193 | if (out != NULL) {
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194 | *out << getType()->getSymbol() << "\t" << at(0) << "\t" << at(1) << "\t" << at(2) << "\t" << endl;
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195 | return true;
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196 | } else
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197 | return false;
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198 | };
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199 |
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200 | /** Output of a single atom as one line in xyz file.
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201 | * \param *out stream to output to
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202 | * \param *ElementNo array with ion type number in the config file this atom's element shall have
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203 | * \param *AtomNo array with atom number in the config file this atom shall have, is increase by one automatically
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204 | * \param step Trajectory time step to output
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205 | * \return true - \a *out present, false - \a *out is NULL
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206 | */
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207 | bool atom::OutputTrajectory(ofstream * const out, const enumeration<const element*> &elementLookup, int *AtomNo, const int step) const
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208 | {
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209 | AtomNo[getType()->getAtomicNumber()]++;
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210 | if (out != NULL) {
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211 | const element *elemental = getType();
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212 | ASSERT(elementLookup.there.find(elemental)!=elementLookup.there.end(),"Type of this atom was not in the formula upon enumeration");
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213 | *out << "Ion_Type" << elementLookup.there.find(elemental)->second << "_" << AtomNo[getType()->getAtomicNumber()] << "\t" << fixed << setprecision(9) << showpoint;
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214 | *out << getPositionAtStep(step)[0] << "\t" << getPositionAtStep(step)[1] << "\t" << getPositionAtStep(step)[2];
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215 | *out << "\t" << (int)(getFixedIon());
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216 | if (getAtomicVelocityAtStep(step).Norm() > MYEPSILON)
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217 | *out << "\t" << scientific << setprecision(6) << getAtomicVelocityAtStep(step)[0] << "\t" << getAtomicVelocityAtStep(step)[1] << "\t" << getAtomicVelocityAtStep(step)[2] << "\t";
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218 | if (getAtomicForceAtStep(step).Norm() > MYEPSILON)
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219 | *out << "\t" << scientific << setprecision(6) << getAtomicForceAtStep(step)[0] << "\t" << getAtomicForceAtStep(step)[1] << "\t" << getAtomicForceAtStep(step)[2] << "\t";
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220 | *out << "\t# Number in molecule " << getNr() << endl;
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221 | return true;
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222 | } else
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223 | return false;
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224 | };
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225 |
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226 | /** Output of a single atom as one lin in xyz file.
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227 | * \param *out stream to output to
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228 | * \param step Trajectory time step to output
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229 | * \return true - \a *out present, false - \a *out is NULL
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230 | */
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231 | bool atom::OutputTrajectoryXYZ(ofstream * const out, const int step) const
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232 | {
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233 | if (out != NULL) {
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234 | *out << getType()->getSymbol() << "\t";
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235 | *out << getPositionAtStep(step)[0] << "\t";
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236 | *out << getPositionAtStep(step)[1] << "\t";
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237 | *out << getPositionAtStep(step)[2] << endl;
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238 | return true;
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239 | } else
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240 | return false;
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241 | };
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242 |
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243 | /** Outputs the MPQC configuration line for this atom.
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244 | * \param *out output stream
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245 | * \param *center center of molecule subtracted from position
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246 | * \param *AtomNo pointer to atom counter that is increased by one
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247 | */
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248 | void atom::OutputMPQCLine(ostream * const out, const Vector *center) const
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249 | {
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250 | Vector recentered(getPosition());
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251 | recentered -= *center;
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252 | *out << "\t\t" << getType()->getSymbol() << " [ " << recentered[0] << "\t" << recentered[1] << "\t" << recentered[2] << " ]" << endl;
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253 | };
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254 |
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255 | /** Compares the indices of \a this atom with a given \a ptr.
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256 | * \param ptr atom to compare index against
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257 | * \return true - this one's is smaller, false - not
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258 | */
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259 | bool atom::Compare(const atom &ptr) const
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260 | {
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261 | if (getNr() < ptr.getNr())
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262 | return true;
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263 | else
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264 | return false;
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265 | };
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266 |
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267 | /** Returns squared distance to a given vector.
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268 | * \param origin vector to calculate distance to
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269 | * \return distance squared
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270 | */
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271 | double atom::DistanceSquaredToVector(const Vector &origin) const
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272 | {
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273 | return DistanceSquared(origin);
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274 | };
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275 |
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276 | /** Returns distance to a given vector.
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277 | * \param origin vector to calculate distance to
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278 | * \return distance
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279 | */
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280 | double atom::DistanceToVector(const Vector &origin) const
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281 | {
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282 | return distance(origin);
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283 | };
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284 |
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285 | /** Initialises the component number array.
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286 | * Size is set to atom::ListOfBonds.size()+1 (last is th encode end by -1)
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287 | */
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288 | void atom::InitComponentNr()
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289 | {
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290 | if (ComponentNr != NULL)
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291 | delete[](ComponentNr);
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292 | const BondList& ListOfBonds = getListOfBonds();
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293 | ComponentNr = new int[ListOfBonds.size()+1];
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294 | for (int i=ListOfBonds.size()+1;i--;)
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295 | ComponentNr[i] = -1;
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296 | };
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297 |
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298 | void atom::resetGraphNr(){
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299 | GraphNr=-1;
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300 | }
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301 |
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302 | std::ostream & atom::operator << (std::ostream &ost) const
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303 | {
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304 | ParticleInfo::operator<<(ost);
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305 | ost << "," << getPosition();
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306 | return ost;
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307 | }
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308 |
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309 | std::ostream & operator << (std::ostream &ost, const atom &a)
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310 | {
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311 | a.ParticleInfo::operator<<(ost);
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312 | ost << "," << a.getPosition();
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313 | return ost;
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314 | }
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315 |
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316 | bool operator < (atom &a, atom &b)
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317 | {
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318 | return a.Compare(b);
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319 | };
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320 |
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321 | World *atom::getWorld(){
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322 | return world;
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323 | }
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324 |
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325 | void atom::setWorld(World* _world){
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326 | world = _world;
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327 | }
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328 |
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329 | bool atom::changeId(atomId_t newId){
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330 | // first we move ourselves in the world
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331 | // the world lets us know if that succeeded
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332 | if(world->changeAtomId(id,newId,this)){
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333 | id = newId;
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334 | return true;
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335 | }
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336 | else{
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337 | return false;
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338 | }
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339 | }
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340 |
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341 | void atom::setId(atomId_t _id) {
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342 | id=_id;
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343 | }
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344 |
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345 | atomId_t atom::getId() const {
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346 | return id;
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347 | }
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348 |
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349 | /** Makes the atom be contained in the new molecule \a *_mol.
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350 | * Uses atom::removeFromMolecule() to delist from old molecule.
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351 | * \param *_mol pointer to new molecule
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352 | */
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353 | void atom::setMolecule(molecule *_mol){
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354 | // take this atom from the old molecule
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355 | removeFromMolecule();
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356 | mol = _mol;
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357 | if(!mol->containsAtom(this)){
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358 | mol->insert(this);
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359 | }
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360 | }
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361 |
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362 | /** Returns pointer to the molecule which atom belongs to.
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363 | * \return containing molecule
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364 | */
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365 | molecule* atom::getMolecule() const {
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366 | return mol;
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367 | }
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368 |
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369 | /** Erases the atom in atom::mol's list of atoms and sets it to zero.
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370 | */
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371 | void atom::removeFromMolecule(){
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372 | if(mol){
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373 | if(mol->containsAtom(this)){
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374 | mol->erase(this);
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375 | }
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376 | mol=0;
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377 | }
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378 | }
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379 |
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380 | int atom::getNr() const{
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381 | return ParticleInfo::getNr();
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382 | }
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383 |
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384 | atom* NewAtom(atomId_t _id){
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385 | atom * res =new atom();
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386 | res->setId(_id);
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387 | return res;
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388 | }
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389 |
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390 | void DeleteAtom(atom* atom){
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391 | delete atom;
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392 | }
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393 |
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394 | bool compareAtomElements(atom* atom1,atom* atom2){
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395 | return atom1->getType()->getNumber() < atom2->getType()->getNumber();
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396 | }
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