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) 2010-2012 University of Bonn. All rights reserved.
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5 | *
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6 | *
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7 | * This file is part of MoleCuilder.
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8 | *
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9 | * MoleCuilder is free software: you can redistribute it and/or modify
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10 | * it under the terms of the GNU General Public License as published by
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11 | * the Free Software Foundation, either version 2 of the License, or
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12 | * (at your option) any later version.
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13 | *
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14 | * MoleCuilder is distributed in the hope that it will be useful,
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15 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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16 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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17 | * GNU General Public License for more details.
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18 | *
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19 | * You should have received a copy of the GNU General Public License
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20 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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21 | */
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22 |
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23 | /*
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24 | * atom_atominfo.cpp
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25 | *
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26 | * Created on: Oct 19, 2009
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27 | * Author: heber
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28 | */
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29 |
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30 | // include config.h
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31 | #ifdef HAVE_CONFIG_H
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32 | #include <config.h>
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33 | #endif
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34 |
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35 | #include "CodePatterns/MemDebug.hpp"
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36 |
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37 | #include "CodePatterns/Verbose.hpp"
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38 |
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39 | #include "atom_atominfo.hpp"
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40 | #include "CodePatterns/Log.hpp"
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41 | #include "config.hpp"
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42 | #include "Element/element.hpp"
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43 | #include "Element/periodentafel.hpp"
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44 | #include "Fragmentation/ForceMatrix.hpp"
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45 | #include "World.hpp"
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46 | #include "WorldTime.hpp"
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47 |
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48 | #include <iomanip>
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49 |
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50 | /** Constructor of class AtomInfo.
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51 | */
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52 | AtomInfo::AtomInfo() :
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53 | AtomicElement(1),
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54 | FixedIon(false),
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55 | charge(0.)
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56 | {
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57 | AtomicPosition.reserve(1);
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58 | AtomicPosition.push_back(zeroVec);
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59 | AtomicVelocity.reserve(1);
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60 | AtomicVelocity.push_back(zeroVec);
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61 | AtomicForce.reserve(1);
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62 | AtomicForce.push_back(zeroVec);
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63 |
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64 | };
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65 |
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66 | /** Copy constructor of class AtomInfo.
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67 | */
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68 | AtomInfo::AtomInfo(const AtomInfo &_atom) :
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69 | AtomicPosition(_atom.AtomicPosition),
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70 | AtomicElement(_atom.AtomicElement),
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71 | FixedIon(_atom.FixedIon),
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72 | charge(_atom.charge)
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73 | {
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74 | AtomicVelocity.reserve(1);
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75 | AtomicVelocity.push_back(zeroVec);
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76 | AtomicForce.reserve(1);
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77 | AtomicForce.push_back(zeroVec);
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78 | };
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79 |
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80 | AtomInfo::AtomInfo(const VectorInterface &_v) :
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81 | AtomicElement(1),
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82 | FixedIon(false),
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83 | charge(0.)
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84 | {
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85 | if (AtomicPosition.size() < 1)
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86 | AtomicPosition.resize(1);
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87 | AtomicPosition[0] = _v.getPosition();
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88 | AtomicVelocity.reserve(1);
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89 | AtomicVelocity.push_back(zeroVec);
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90 | AtomicForce.reserve(1);
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91 | AtomicForce.push_back(zeroVec);
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92 | };
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93 |
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94 | /** Destructor of class AtomInfo.
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95 | */
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96 | AtomInfo::~AtomInfo()
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97 | {
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98 | };
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99 |
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100 | void AtomInfo::AppendTrajectoryStep()
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101 | {
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102 | NOTIFY(TrajectoryChanged);
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103 | AtomicPosition.push_back(zeroVec);
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104 | AtomicVelocity.push_back(zeroVec);
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105 | AtomicForce.push_back(zeroVec);
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106 | LOG(5,"AtomInfo::AppendTrajectoryStep() called, size is ("
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107 | << AtomicPosition.size() << ","
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108 | << AtomicVelocity.size() << ","
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109 | << AtomicForce.size() << ")");
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110 | }
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111 |
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112 | const element *AtomInfo::getType() const
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113 | {
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114 | const element *elem = World::getInstance().getPeriode()->FindElement(AtomicElement);
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115 | return elem;
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116 | }
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117 |
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118 | const element &AtomInfo::getElement() const
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119 | {
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120 | const element &elem = *World::getInstance().getPeriode()->FindElement(AtomicElement);
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121 | return elem;
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122 | }
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123 |
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124 | atomicNumber_t AtomInfo::getElementNo() const
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125 | {
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126 | return AtomicElement;
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127 | }
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128 |
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129 | const double& AtomInfo::operator[](size_t i) const
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130 | {
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131 | ASSERT(AtomicPosition.size() > WorldTime::getTime(),
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132 | "AtomInfo::operator[]() - Access out of range: "
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133 | +toString(WorldTime::getTime())
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134 | +" not in [0,"+toString(AtomicPosition.size())+").");
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135 | return AtomicPosition[WorldTime::getTime()][i];
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136 | }
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137 |
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138 | const double& AtomInfo::at(size_t i) const
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139 | {
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140 | ASSERT(AtomicPosition.size() > WorldTime::getTime(),
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141 | "AtomInfo::at() - Access out of range: "
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142 | +toString(WorldTime::getTime())
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143 | +" not in [0,"+toString(AtomicPosition.size())+").");
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144 | return AtomicPosition[WorldTime::getTime()].at(i);
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145 | }
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146 |
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147 | const double& AtomInfo::atStep(size_t i, unsigned int _step) const
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148 | {
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149 | ASSERT(AtomicPosition.size() > _step,
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150 | "AtomInfo::atStep() - Access out of range: "
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151 | +toString(_step)
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152 | +" not in [0,"+toString(AtomicPosition.size())+").");
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153 | return AtomicPosition[_step].at(i);
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154 | }
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155 |
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156 | void AtomInfo::set(size_t i, const double value)
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157 | {
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158 | OBSERVE;
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159 | NOTIFY(AtomObservable::PositionChanged);
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160 | ASSERT(AtomicPosition.size() > WorldTime::getTime(),
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161 | "AtomInfo::set() - Access out of range: "
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162 | +toString(WorldTime::getTime())
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163 | +" not in [0,"+toString(AtomicPosition.size())+").");
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164 | AtomicPosition[WorldTime::getTime()].at(i) = value;
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165 | }
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166 |
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167 | const Vector& AtomInfo::getPosition() const
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168 | {
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169 | ASSERT(AtomicPosition.size() > WorldTime::getTime(),
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170 | "AtomInfo::getPosition() - Access out of range: "
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171 | +toString(WorldTime::getTime())
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172 | +" not in [0,"+toString(AtomicPosition.size())+").");
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173 | return AtomicPosition[WorldTime::getTime()];
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174 | }
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175 |
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176 | const Vector& AtomInfo::getPositionAtStep(const unsigned int _step) const
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177 | {
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178 | ASSERT(_step < AtomicPosition.size(),
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179 | "AtomInfo::getPositionAtStep() - Access out of range: "
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180 | +toString(_step)
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181 | +" not in [0,"+toString(AtomicPosition.size())+").");
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182 | return AtomicPosition[_step];
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183 | }
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184 |
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185 | void AtomInfo::setType(const element* _type)
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186 | {
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187 | if (_type->getAtomicNumber() != AtomicElement) {
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188 | OBSERVE;
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189 | NOTIFY(AtomObservable::ElementChanged);
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190 | AtomicElement = _type->getAtomicNumber();
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191 | }
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192 | }
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193 |
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194 | void AtomInfo::setType(const int Z)
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195 | {
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196 | const element *elem = World::getInstance().getPeriode()->FindElement(Z);
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197 | if (elem != NULL) {
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198 | OBSERVE;
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199 | NOTIFY(AtomObservable::ElementChanged);
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200 | AtomicElement = Z;
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201 | }
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202 | }
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203 |
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204 | //Vector& AtomInfo::getAtomicVelocity()
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205 | //{
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206 | // return AtomicVelocity[0];
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207 | //}
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208 |
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209 | //Vector& AtomInfo::getAtomicVelocity(const int _step)
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210 | //{
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211 | // ASSERT(_step < AtomicVelocity.size(),
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212 | // "AtomInfo::getAtomicVelocity() - Access out of range.");
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213 | // return AtomicVelocity[_step];
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214 | //}
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215 |
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216 | const Vector& AtomInfo::getAtomicVelocity() const
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217 | {
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218 | ASSERT(AtomicVelocity.size() > 0,
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219 | "AtomInfo::getAtomicVelocity() - Access out of range: "
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220 | +toString(WorldTime::getTime())
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221 | +" not in [0,"+toString(AtomicPosition.size())+").");
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222 | return AtomicVelocity[WorldTime::getTime()];
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223 | }
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224 |
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225 | const Vector& AtomInfo::getAtomicVelocityAtStep(const unsigned int _step) const
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226 | {
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227 | ASSERT(_step < AtomicVelocity.size(),
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228 | "AtomInfo::getAtomicVelocity() - Access out of range: "
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229 | +toString(_step)
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230 | +" not in [0,"+toString(AtomicPosition.size())+").");
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231 | return AtomicVelocity[_step];
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232 | }
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233 |
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234 | void AtomInfo::setAtomicVelocity(const Vector &_newvelocity)
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235 | {
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236 | OBSERVE;
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237 | NOTIFY(AtomObservable::VelocityChanged);
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238 | ASSERT(WorldTime::getTime() < AtomicVelocity.size(),
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239 | "AtomInfo::setAtomicVelocity() - Access out of range: "
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240 | +toString(WorldTime::getTime())
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241 | +" not in [0,"+toString(AtomicPosition.size())+").");
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242 | AtomicVelocity[WorldTime::getTime()] = _newvelocity;
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243 | }
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244 |
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245 | void AtomInfo::setAtomicVelocityAtStep(const unsigned int _step, const Vector &_newvelocity)
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246 | {
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247 | OBSERVE;
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248 | if (WorldTime::getTime() == _step)
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249 | NOTIFY(AtomObservable::VelocityChanged);
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250 | const unsigned int size = AtomicVelocity.size();
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251 | ASSERT(_step <= size,
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252 | "AtomInfo::setAtomicVelocityAtStep() - Access out of range: "
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253 | +toString(_step)
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254 | +" not in [0,"+toString(size)+"].");
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255 | if(_step < size) {
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256 | AtomicVelocity[_step] = _newvelocity;
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257 | } else if (_step == size) {
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258 | UpdateSteps();
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259 | AtomicVelocity[_step] = _newvelocity;
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260 | }
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261 | }
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262 |
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263 | const Vector& AtomInfo::getAtomicForce() const
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264 | {
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265 | ASSERT(WorldTime::getTime() < AtomicForce.size(),
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266 | "AtomInfo::getAtomicForce() - Access out of range: "
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267 | +toString(WorldTime::getTime())
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268 | +" not in [0,"+toString(AtomicPosition.size())+").");
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269 | return AtomicForce[WorldTime::getTime()];
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270 | }
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271 |
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272 | const Vector& AtomInfo::getAtomicForceAtStep(const unsigned int _step) const
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273 | {
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274 | ASSERT(_step < AtomicForce.size(),
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275 | "AtomInfo::getAtomicForce() - Access out of range: "
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276 | +toString(_step)
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277 | +" not in [0,"+toString(AtomicPosition.size())+").");
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278 | return AtomicForce[_step];
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279 | }
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280 |
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281 | void AtomInfo::setAtomicForce(const Vector &_newforce)
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282 | {
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283 | OBSERVE;
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284 | NOTIFY(AtomObservable::ForceChanged);
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285 | ASSERT(WorldTime::getTime() < AtomicForce.size(),
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286 | "AtomInfo::setAtomicForce() - Access out of range: "
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287 | +toString(WorldTime::getTime())
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288 | +" not in [0,"+toString(AtomicPosition.size())+").");
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289 | AtomicForce[WorldTime::getTime()] = _newforce;
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290 | }
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291 |
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292 | void AtomInfo::setAtomicForceAtStep(const unsigned int _step, const Vector &_newforce)
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293 | {
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294 | OBSERVE;
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295 | if (WorldTime::getTime() == _step)
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296 | NOTIFY(AtomObservable::ForceChanged);
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297 | const unsigned int size = AtomicForce.size();
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298 | ASSERT(_step <= size,
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299 | "AtomInfo::setAtomicForce() - Access out of range: "
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300 | +toString(_step)
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301 | +" not in [0,"+toString(AtomicPosition.size())+"].");
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302 | if(_step < size) {
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303 | AtomicForce[_step] = _newforce;
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304 | } else if (_step == size) {
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305 | UpdateSteps();
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306 | AtomicForce[_step] = _newforce;
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307 | }
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308 | }
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309 |
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310 | bool AtomInfo::getFixedIon() const
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311 | {
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312 | return FixedIon;
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313 | }
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314 |
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315 | void AtomInfo::setFixedIon(const bool _fixedion)
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316 | {
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317 | OBSERVE;
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318 | NOTIFY(AtomObservable::PropertyChanged);
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319 | FixedIon = _fixedion;
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320 | }
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321 |
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322 | void AtomInfo::setPosition(const Vector& _vector)
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323 | {
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324 | OBSERVE;
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325 | NOTIFY(AtomObservable::PositionChanged);
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326 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
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327 | "AtomInfo::setPosition() - Access out of range: "
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328 | +toString(WorldTime::getTime())
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329 | +" not in [0,"+toString(AtomicPosition.size())+").");
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330 | AtomicPosition[WorldTime::getTime()] = _vector;
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331 | //cout << "AtomInfo::setPosition: " << getType()->symbol << " at " << getPosition() << endl;
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332 | }
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333 |
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334 | void AtomInfo::setPositionAtStep(unsigned int _step, const Vector& _vector)
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335 | {
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336 | OBSERVE;
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337 | if (WorldTime::getTime() == _step)
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338 | NOTIFY(AtomObservable::PositionChanged);
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339 | const unsigned int size = AtomicPosition.size();
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340 | ASSERT(_step <= size,
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341 | "AtomInfo::setPosition() - Access out of range: "
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342 | +toString(_step)
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343 | +" not in [0,"+toString(size)+"].");
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344 | if(_step < size) {
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345 | AtomicPosition[_step] = _vector;
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346 | } else if (_step == size) {
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347 | UpdateSteps();
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348 | AtomicPosition[_step] = _vector;
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349 | }
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350 | //cout << "AtomInfo::setPosition: " << getType()->symbol << " at " << getPosition() << endl;
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351 | }
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352 |
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353 | const VectorInterface& AtomInfo::operator+=(const Vector& b)
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354 | {
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355 | OBSERVE;
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356 | NOTIFY(AtomObservable::PositionChanged);
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357 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
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358 | "AtomInfo::operator+=() - Access out of range: "
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359 | +toString(WorldTime::getTime())
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360 | +" not in [0,"+toString(AtomicPosition.size())+").");
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361 | AtomicPosition[WorldTime::getTime()] += b;
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362 | return *this;
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363 | }
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364 |
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365 | const VectorInterface& AtomInfo::operator-=(const Vector& b)
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366 | {
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367 | OBSERVE;
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368 | NOTIFY(AtomObservable::PositionChanged);
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369 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
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370 | "AtomInfo::operator-=() - Access out of range: "
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371 | +toString(WorldTime::getTime())
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372 | +" not in [0,"+toString(AtomicPosition.size())+").");
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373 | AtomicPosition[WorldTime::getTime()] -= b;
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374 | return *this;
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375 | }
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376 |
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377 | Vector const AtomInfo::operator+(const Vector& b) const
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378 | {
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379 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
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380 | "AtomInfo::operator+() - Access out of range: "
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381 | +toString(WorldTime::getTime())
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382 | +" not in [0,"+toString(AtomicPosition.size())+").");
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383 | Vector a(AtomicPosition[WorldTime::getTime()]);
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384 | a += b;
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385 | return a;
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386 | }
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387 |
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388 | Vector const AtomInfo::operator-(const Vector& b) const
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389 | {
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390 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
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391 | "AtomInfo::operator-() - Access out of range: "
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392 | +toString(WorldTime::getTime())
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393 | +" not in [0,"+toString(AtomicPosition.size())+").");
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394 | Vector a(AtomicPosition[WorldTime::getTime()]);
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395 | a -= b;
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396 | return a;
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397 | }
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398 |
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399 | double AtomInfo::distance(const Vector &point) const
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400 | {
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401 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
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402 | "AtomInfo::distance() - Access out of range: "
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403 | +toString(WorldTime::getTime())
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404 | +" not in [0,"+toString(AtomicPosition.size())+").");
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405 | return AtomicPosition[WorldTime::getTime()].distance(point);
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406 | }
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407 |
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408 | double AtomInfo::DistanceSquared(const Vector &y) const
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409 | {
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410 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
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411 | "AtomInfo::DistanceSquared() - Access out of range: "
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412 | +toString(WorldTime::getTime())
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413 | +" not in [0,"+toString(AtomicPosition.size())+").");
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414 | return AtomicPosition[WorldTime::getTime()].DistanceSquared(y);
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415 | }
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416 |
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417 | double AtomInfo::distance(const VectorInterface &_atom) const
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418 | {
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419 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
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420 | "AtomInfo::distance() - Access out of range: "
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421 | +toString(WorldTime::getTime())
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422 | +" not in [0,"+toString(AtomicPosition.size())+").");
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423 | return _atom.distance(AtomicPosition[WorldTime::getTime()]);
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424 | }
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425 |
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426 | double AtomInfo::DistanceSquared(const VectorInterface &_atom) const
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427 | {
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428 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
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429 | "AtomInfo::DistanceSquared() - Access out of range: "
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430 | +toString(WorldTime::getTime())
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431 | +" not in [0,"+toString(AtomicPosition.size())+").");
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432 | return _atom.DistanceSquared(AtomicPosition[WorldTime::getTime()]);
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433 | }
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434 |
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435 | VectorInterface &AtomInfo::operator=(const Vector& _vector)
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436 | {
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437 | OBSERVE;
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438 | NOTIFY(AtomObservable::PositionChanged);
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439 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
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440 | "AtomInfo::operator=() - Access out of range: "
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441 | +toString(WorldTime::getTime())
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442 | +" not in [0,"+toString(AtomicPosition.size())+").");
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443 | AtomicPosition[WorldTime::getTime()] = _vector;
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444 | return *this;
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445 | }
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446 |
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447 | void AtomInfo::ScaleAll(const double *factor)
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448 | {
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449 | OBSERVE;
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450 | NOTIFY(AtomObservable::PositionChanged);
|
---|
451 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
|
---|
452 | "AtomInfo::ScaleAll() - Access out of range: "
|
---|
453 | +toString(WorldTime::getTime())
|
---|
454 | +" not in [0,"+toString(AtomicPosition.size())+").");
|
---|
455 | AtomicPosition[WorldTime::getTime()].ScaleAll(factor);
|
---|
456 | }
|
---|
457 |
|
---|
458 | void AtomInfo::ScaleAll(const Vector &factor)
|
---|
459 | {
|
---|
460 | OBSERVE;
|
---|
461 | NOTIFY(AtomObservable::PositionChanged);
|
---|
462 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
|
---|
463 | "AtomInfo::ScaleAll() - Access out of range: "
|
---|
464 | +toString(WorldTime::getTime())
|
---|
465 | +" not in [0,"+toString(AtomicPosition.size())+").");
|
---|
466 | AtomicPosition[WorldTime::getTime()].ScaleAll(factor);
|
---|
467 | }
|
---|
468 |
|
---|
469 | void AtomInfo::Scale(const double factor)
|
---|
470 | {
|
---|
471 | OBSERVE;
|
---|
472 | NOTIFY(AtomObservable::PositionChanged);
|
---|
473 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
|
---|
474 | "AtomInfo::Scale() - Access out of range: "
|
---|
475 | +toString(WorldTime::getTime())
|
---|
476 | +" not in [0,"+toString(AtomicPosition.size())+").");
|
---|
477 | AtomicPosition[WorldTime::getTime()].Scale(factor);
|
---|
478 | }
|
---|
479 |
|
---|
480 | void AtomInfo::Zero()
|
---|
481 | {
|
---|
482 | OBSERVE;
|
---|
483 | NOTIFY(AtomObservable::PositionChanged);
|
---|
484 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
|
---|
485 | "AtomInfo::Zero() - Access out of range: "
|
---|
486 | +toString(WorldTime::getTime())
|
---|
487 | +" not in [0,"+toString(AtomicPosition.size())+").");
|
---|
488 | AtomicPosition[WorldTime::getTime()].Zero();
|
---|
489 | }
|
---|
490 |
|
---|
491 | void AtomInfo::One(const double one)
|
---|
492 | {
|
---|
493 | OBSERVE;
|
---|
494 | NOTIFY(AtomObservable::PositionChanged);
|
---|
495 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
|
---|
496 | "AtomInfo::One() - Access out of range: "
|
---|
497 | +toString(WorldTime::getTime())
|
---|
498 | +" not in [0,"+toString(AtomicPosition.size())+").");
|
---|
499 | AtomicPosition[WorldTime::getTime()].One(one);
|
---|
500 | }
|
---|
501 |
|
---|
502 | void AtomInfo::LinearCombinationOfVectors(const Vector &x1, const Vector &x2, const Vector &x3, const double * const factors)
|
---|
503 | {
|
---|
504 | OBSERVE;
|
---|
505 | NOTIFY(AtomObservable::PositionChanged);
|
---|
506 | ASSERT(WorldTime::getTime() < AtomicPosition.size(),
|
---|
507 | "AtomInfo::LinearCombinationOfVectors() - Access out of range: "
|
---|
508 | +toString(WorldTime::getTime())
|
---|
509 | +" not in [0,"+toString(AtomicPosition.size())+").");
|
---|
510 | AtomicPosition[WorldTime::getTime()].LinearCombinationOfVectors(x1,x2,x3,factors);
|
---|
511 | }
|
---|
512 |
|
---|
513 | /**
|
---|
514 | * returns the kinetic energy of this atom at a given time step
|
---|
515 | */
|
---|
516 | double AtomInfo::getKineticEnergy(const unsigned int _step) const
|
---|
517 | {
|
---|
518 | ASSERT(_step < AtomicPosition.size(),
|
---|
519 | "AtomInfo::getKineticEnergy() - Access out of range: "
|
---|
520 | +toString(WorldTime::getTime())
|
---|
521 | +" not in [0,"+toString(AtomicPosition.size())+").");
|
---|
522 | return getMass() * AtomicVelocity[_step].NormSquared();
|
---|
523 | }
|
---|
524 |
|
---|
525 | Vector AtomInfo::getMomentum(const unsigned int _step) const
|
---|
526 | {
|
---|
527 | ASSERT(_step < AtomicPosition.size(),
|
---|
528 | "AtomInfo::getMomentum() - Access out of range: "
|
---|
529 | +toString(WorldTime::getTime())
|
---|
530 | +" not in [0,"+toString(AtomicPosition.size())+").");
|
---|
531 | return getMass()*AtomicVelocity[_step];
|
---|
532 | }
|
---|
533 |
|
---|
534 | /** Extends the trajectory STL vector to the new size.
|
---|
535 | * Does nothing if \a MaxSteps is smaller than current size.
|
---|
536 | * \param MaxSteps
|
---|
537 | */
|
---|
538 | void AtomInfo::ResizeTrajectory(size_t MaxSteps)
|
---|
539 | {
|
---|
540 | for (;AtomicPosition.size() <= (unsigned int)(MaxSteps);)
|
---|
541 | UpdateSteps();
|
---|
542 | }
|
---|
543 |
|
---|
544 | size_t AtomInfo::getTrajectorySize() const
|
---|
545 | {
|
---|
546 | return AtomicPosition.size();
|
---|
547 | }
|
---|
548 |
|
---|
549 | double AtomInfo::getMass() const
|
---|
550 | {
|
---|
551 | return getType()->getMass();
|
---|
552 | }
|
---|
553 |
|
---|
554 | /** Copies a given trajectory step \a src onto another \a dest
|
---|
555 | * \param dest index of destination step
|
---|
556 | * \param src index of source step
|
---|
557 | */
|
---|
558 | void AtomInfo::CopyStepOnStep(const unsigned int dest, const unsigned int src)
|
---|
559 | {
|
---|
560 | if (dest == src) // self assignment check
|
---|
561 | return;
|
---|
562 |
|
---|
563 | if (WorldTime::getTime() == dest){
|
---|
564 | NOTIFY(AtomObservable::PositionChanged);
|
---|
565 | NOTIFY(AtomObservable::VelocityChanged);
|
---|
566 | NOTIFY(AtomObservable::ForceChanged);
|
---|
567 | }
|
---|
568 |
|
---|
569 | ASSERT(dest < AtomicPosition.size(),
|
---|
570 | "AtomInfo::CopyStepOnStep() - destination outside of current trajectory array: "
|
---|
571 | +toString(dest)
|
---|
572 | +" not in [0,"+toString(AtomicPosition.size())+").");
|
---|
573 | ASSERT(src < AtomicPosition.size(),
|
---|
574 | "AtomInfo::CopyStepOnStep() - source outside of current trajectory array: "
|
---|
575 | +toString(src)
|
---|
576 | +" not in [0,"+toString(AtomicPosition.size())+").");
|
---|
577 | for (int n=NDIM;n--;) {
|
---|
578 | AtomicPosition.at(dest)[n] = AtomicPosition.at(src)[n];
|
---|
579 | AtomicVelocity.at(dest)[n] = AtomicVelocity.at(src)[n];
|
---|
580 | AtomicForce.at(dest)[n] = AtomicForce.at(src)[n];
|
---|
581 | }
|
---|
582 | };
|
---|
583 |
|
---|
584 | /** Performs a velocity verlet update of the position at \a NextStep from \a LastStep information only.
|
---|
585 | *
|
---|
586 | * We calculate \f$x(t + \delta t) = x(t) + v(t)* \delta t + .5 * \delta t * \delta t * F(t)/m \f$.
|
---|
587 | *
|
---|
588 | *
|
---|
589 | * \param NextStep index of sequential step to set
|
---|
590 | * \param Deltat time step width
|
---|
591 | * \param IsAngstroem whether the force's underlying unit of length is angstroem or bohr radii
|
---|
592 | */
|
---|
593 | void AtomInfo::VelocityVerletUpdateX(int nr, const unsigned int NextStep, double Deltat, bool IsAngstroem)
|
---|
594 | {
|
---|
595 | const unsigned int LastStep = NextStep == 0 ? 0 : NextStep-1;
|
---|
596 |
|
---|
597 | LOG(2, "INFO: Particle that currently " << *this);
|
---|
598 | LOG(2, "INFO: Integrating position with mass=" << getMass() << " and Deltat="
|
---|
599 | << Deltat << " at NextStep=" << NextStep);
|
---|
600 |
|
---|
601 | // update position
|
---|
602 | {
|
---|
603 | Vector tempVector = getPositionAtStep(LastStep);
|
---|
604 | LOG(4, "INFO: initial position from last step " << setprecision(4) << tempVector);
|
---|
605 | tempVector += Deltat*(getAtomicVelocityAtStep(LastStep)); // s(t) = s(0) + v * deltat + 1/2 a * deltat^2
|
---|
606 | LOG(4, "INFO: position with velocity " << getAtomicVelocityAtStep(LastStep) << " from last step " << tempVector);
|
---|
607 | tempVector += .5*Deltat*Deltat*(getAtomicForceAtStep(LastStep))*(1./getMass()); // F = m * a and s =
|
---|
608 | LOG(4, "INFO: position with force " << getAtomicForceAtStep(LastStep) << " from last step " << tempVector);
|
---|
609 | setPositionAtStep(NextStep, tempVector);
|
---|
610 | LOG(3, "INFO: Position at step " << NextStep << " set to " << tempVector);
|
---|
611 | }
|
---|
612 | };
|
---|
613 |
|
---|
614 | /** Performs a velocity verlet update of the velocity at \a NextStep.
|
---|
615 | *
|
---|
616 | * \note forces at NextStep should have been calculated based on position at NextStep prior
|
---|
617 | * to calling this function.
|
---|
618 | *
|
---|
619 | * We calculate \f$v(t) = v(t - \delta t) + \delta _t * .5 * (F(t - \delta t) + F(t))/m \f$.
|
---|
620 | *
|
---|
621 | * Parameters are according to those in configuration class.
|
---|
622 | * \param NextStep index of sequential step to set
|
---|
623 | * \param Deltat time step width
|
---|
624 | * \param IsAngstroem whether the force's underlying unit of length is angstroem or bohr radii
|
---|
625 | */
|
---|
626 | void AtomInfo::VelocityVerletUpdateU(int nr, const unsigned int NextStep, double Deltat, bool IsAngstroem)
|
---|
627 | {
|
---|
628 | const unsigned int LastStep = NextStep == 0 ? 0 : NextStep-1;
|
---|
629 |
|
---|
630 | LOG(2, "INFO: Particle that currently " << *this);
|
---|
631 | LOG(2, "INFO: Integrating velocity with mass=" << getMass() << " and Deltat="
|
---|
632 | << Deltat << " at NextStep=" << NextStep);
|
---|
633 |
|
---|
634 | // Update U
|
---|
635 | {
|
---|
636 | Vector tempVector = getAtomicVelocityAtStep(LastStep);
|
---|
637 | LOG(4, "INFO: initial velocity from last step " << tempVector);
|
---|
638 | tempVector += Deltat * .5*(getAtomicForceAtStep(LastStep)+getAtomicForceAtStep(NextStep))*(1./getMass()); // v = F/m * t
|
---|
639 | LOG(4, "INFO: Velocity with force from last " << getAtomicForceAtStep(LastStep)
|
---|
640 | << " and present " << getAtomicForceAtStep(NextStep) << " step " << tempVector);
|
---|
641 | setAtomicVelocityAtStep(NextStep, tempVector);
|
---|
642 | LOG(3, "INFO: Velocity at step " << NextStep << " set to " << tempVector);
|
---|
643 | }
|
---|
644 | };
|
---|
645 |
|
---|
646 | //const AtomInfo& operator*=(AtomInfo& a, const double m)
|
---|
647 | //{
|
---|
648 | // a.Scale(m);
|
---|
649 | // return a;
|
---|
650 | //}
|
---|
651 | //
|
---|
652 | //AtomInfo const operator*(const AtomInfo& a, const double m)
|
---|
653 | //{
|
---|
654 | // AtomInfo copy(a);
|
---|
655 | // copy *= m;
|
---|
656 | // return copy;
|
---|
657 | //}
|
---|
658 | //
|
---|
659 | //AtomInfo const operator*(const double m, const AtomInfo& a)
|
---|
660 | //{
|
---|
661 | // AtomInfo copy(a);
|
---|
662 | // copy *= m;
|
---|
663 | // return copy;
|
---|
664 | //}
|
---|
665 |
|
---|
666 | std::ostream & AtomInfo::operator << (std::ostream &ost) const
|
---|
667 | {
|
---|
668 | return (ost << getPosition());
|
---|
669 | }
|
---|
670 |
|
---|
671 | std::ostream & operator << (std::ostream &ost, const AtomInfo &a)
|
---|
672 | {
|
---|
673 | const size_t terminalstep = a.getTrajectorySize()-1;
|
---|
674 | if (terminalstep) {
|
---|
675 | ost << "starts at "
|
---|
676 | << a.getPositionAtStep(0) << " and ends at "
|
---|
677 | << a.getPositionAtStep(terminalstep)
|
---|
678 | << " at time step " << terminalstep;
|
---|
679 | } else {
|
---|
680 | ost << "is at "
|
---|
681 | << a.getPositionAtStep(0) << " with a single time step only";
|
---|
682 | }
|
---|
683 | return ost;
|
---|
684 | }
|
---|
685 |
|
---|