| 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); | 
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| 451 | ASSERT(WorldTime::getTime() < AtomicPosition.size(), | 
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| 452 | "AtomInfo::ScaleAll() - Access out of range: " | 
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| 453 | +toString(WorldTime::getTime()) | 
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| 454 | +" not in [0,"+toString(AtomicPosition.size())+")."); | 
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| 455 | AtomicPosition[WorldTime::getTime()].ScaleAll(factor); | 
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| 456 | } | 
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| 457 |  | 
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| 458 | void AtomInfo::ScaleAll(const Vector &factor) | 
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| 459 | { | 
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| 460 | OBSERVE; | 
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| 461 | NOTIFY(AtomObservable::PositionChanged); | 
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| 462 | ASSERT(WorldTime::getTime() < AtomicPosition.size(), | 
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| 463 | "AtomInfo::ScaleAll() - Access out of range: " | 
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| 464 | +toString(WorldTime::getTime()) | 
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| 465 | +" not in [0,"+toString(AtomicPosition.size())+")."); | 
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| 466 | AtomicPosition[WorldTime::getTime()].ScaleAll(factor); | 
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| 467 | } | 
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| 468 |  | 
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| 469 | void AtomInfo::Scale(const double factor) | 
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| 470 | { | 
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| 471 | OBSERVE; | 
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| 472 | NOTIFY(AtomObservable::PositionChanged); | 
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| 473 | ASSERT(WorldTime::getTime() < AtomicPosition.size(), | 
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| 474 | "AtomInfo::Scale() - Access out of range: " | 
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| 475 | +toString(WorldTime::getTime()) | 
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| 476 | +" not in [0,"+toString(AtomicPosition.size())+")."); | 
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| 477 | AtomicPosition[WorldTime::getTime()].Scale(factor); | 
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| 478 | } | 
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| 479 |  | 
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| 480 | void AtomInfo::Zero() | 
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| 481 | { | 
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| 482 | OBSERVE; | 
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| 483 | NOTIFY(AtomObservable::PositionChanged); | 
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| 484 | ASSERT(WorldTime::getTime() < AtomicPosition.size(), | 
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| 485 | "AtomInfo::Zero() - Access out of range: " | 
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| 486 | +toString(WorldTime::getTime()) | 
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| 487 | +" not in [0,"+toString(AtomicPosition.size())+")."); | 
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| 488 | AtomicPosition[WorldTime::getTime()].Zero(); | 
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| 489 | } | 
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| 490 |  | 
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| 491 | void AtomInfo::One(const double one) | 
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| 492 | { | 
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| 493 | OBSERVE; | 
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| 494 | NOTIFY(AtomObservable::PositionChanged); | 
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| 495 | ASSERT(WorldTime::getTime() < AtomicPosition.size(), | 
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| 496 | "AtomInfo::One() - Access out of range: " | 
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| 497 | +toString(WorldTime::getTime()) | 
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| 498 | +" not in [0,"+toString(AtomicPosition.size())+")."); | 
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| 499 | AtomicPosition[WorldTime::getTime()].One(one); | 
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| 500 | } | 
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| 501 |  | 
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| 502 | void AtomInfo::LinearCombinationOfVectors(const Vector &x1, const Vector &x2, const Vector &x3, const double * const factors) | 
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| 503 | { | 
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| 504 | OBSERVE; | 
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| 505 | NOTIFY(AtomObservable::PositionChanged); | 
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| 506 | ASSERT(WorldTime::getTime() < AtomicPosition.size(), | 
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| 507 | "AtomInfo::LinearCombinationOfVectors() - Access out of range: " | 
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| 508 | +toString(WorldTime::getTime()) | 
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| 509 | +" not in [0,"+toString(AtomicPosition.size())+")."); | 
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| 510 | AtomicPosition[WorldTime::getTime()].LinearCombinationOfVectors(x1,x2,x3,factors); | 
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| 511 | } | 
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| 512 |  | 
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| 513 | /** | 
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| 514 | *  returns the kinetic energy of this atom at a given time step | 
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| 515 | */ | 
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| 516 | double AtomInfo::getKineticEnergy(const unsigned int _step) const | 
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| 517 | { | 
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| 518 | ASSERT(_step < AtomicPosition.size(), | 
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| 519 | "AtomInfo::getKineticEnergy() - Access out of range: " | 
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| 520 | +toString(WorldTime::getTime()) | 
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| 521 | +" not in [0,"+toString(AtomicPosition.size())+")."); | 
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| 522 | return getMass() * AtomicVelocity[_step].NormSquared(); | 
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| 523 | } | 
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| 524 |  | 
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| 525 | Vector AtomInfo::getMomentum(const unsigned int _step) const | 
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| 526 | { | 
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| 527 | ASSERT(_step < AtomicPosition.size(), | 
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| 528 | "AtomInfo::getMomentum() - Access out of range: " | 
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| 529 | +toString(WorldTime::getTime()) | 
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| 530 | +" not in [0,"+toString(AtomicPosition.size())+")."); | 
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| 531 | return getMass()*AtomicVelocity[_step]; | 
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| 532 | } | 
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| 533 |  | 
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| 534 | /** Extends the trajectory STL vector to the new size. | 
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| 535 | * Does nothing if \a MaxSteps is smaller than current size. | 
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| 536 | * \param MaxSteps | 
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| 537 | */ | 
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| 538 | void AtomInfo::ResizeTrajectory(size_t MaxSteps) | 
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| 539 | { | 
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| 540 | for (;AtomicPosition.size() <= (unsigned int)(MaxSteps);) | 
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| 541 | UpdateSteps(); | 
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| 542 | } | 
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| 543 |  | 
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| 544 | size_t AtomInfo::getTrajectorySize() const | 
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| 545 | { | 
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| 546 | return AtomicPosition.size(); | 
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| 547 | } | 
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| 548 |  | 
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| 549 | double AtomInfo::getMass() const | 
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| 550 | { | 
|---|
| 551 | return getType()->getMass(); | 
|---|
| 552 | } | 
|---|
| 553 |  | 
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| 554 | /** Copies a given trajectory step \a src onto another \a dest | 
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| 555 | * \param dest index of destination step | 
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| 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); | 
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| 565 | NOTIFY(AtomObservable::VelocityChanged); | 
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| 566 | NOTIFY(AtomObservable::ForceChanged); | 
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| 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 |  | 
|---|