| [bcf653] | 1 | /* | 
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|  | 2 | * Project: MoleCuilder | 
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|  | 3 | * Description: creates and alters molecular systems | 
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| [0aa122] | 4 | * Copyright (C)  2010-2012 University of Bonn. All rights reserved. | 
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| [94d5ac6] | 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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| [bcf653] | 21 | */ | 
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|  | 22 |  | 
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| [6b919f8] | 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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| [bf3817] | 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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| [ad011c] | 35 | #include "CodePatterns/MemDebug.hpp" | 
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| [112b09] | 36 |  | 
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| [6625c3] | 37 | #include "CodePatterns/Verbose.hpp" | 
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| [08a0f52] | 38 |  | 
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|  | 39 | #include "atom_atominfo.hpp" | 
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|  | 40 | #include "CodePatterns/Log.hpp" | 
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| [6625c3] | 41 | #include "config.hpp" | 
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| [3bdb6d] | 42 | #include "Element/element.hpp" | 
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|  | 43 | #include "Element/periodentafel.hpp" | 
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| [a9b86d] | 44 | #include "Fragmentation/ForceMatrix.hpp" | 
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| [f16a4b] | 45 | #include "World.hpp" | 
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| [1b558c] | 46 | #include "WorldTime.hpp" | 
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| [6b919f8] | 47 |  | 
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| [435065] | 48 | #include <iomanip> | 
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|  | 49 |  | 
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| [6b919f8] | 50 | /** Constructor of class AtomInfo. | 
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|  | 51 | */ | 
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| [97b825] | 52 | AtomInfo::AtomInfo() : | 
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| [606c24] | 53 | AtomicElement(1), | 
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| [2034f3] | 54 | FixedIon(false), | 
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|  | 55 | charge(0.) | 
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| [54b42e] | 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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| [08a0f52] | 63 |  | 
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| [54b42e] | 64 | }; | 
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| [d74077] | 65 |  | 
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|  | 66 | /** Copy constructor of class AtomInfo. | 
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|  | 67 | */ | 
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| [97b825] | 68 | AtomInfo::AtomInfo(const AtomInfo &_atom) : | 
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|  | 69 | AtomicPosition(_atom.AtomicPosition), | 
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| [6625c3] | 70 | AtomicElement(_atom.AtomicElement), | 
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| [2034f3] | 71 | FixedIon(_atom.FixedIon), | 
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|  | 72 | charge(_atom.charge) | 
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| [6625c3] | 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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| [d74077] | 79 |  | 
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| [97b825] | 80 | AtomInfo::AtomInfo(const VectorInterface &_v) : | 
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| [606c24] | 81 | AtomicElement(1), | 
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| [2034f3] | 82 | FixedIon(false), | 
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|  | 83 | charge(0.) | 
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| [54b42e] | 84 | { | 
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| [606c24] | 85 | if (AtomicPosition.size() < 1) | 
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|  | 86 | AtomicPosition.resize(1); | 
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| [54b42e] | 87 | AtomicPosition[0] = _v.getPosition(); | 
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| [6625c3] | 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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| [54b42e] | 92 | }; | 
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| [6b919f8] | 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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| [e2373df] | 100 | void AtomInfo::AppendTrajectoryStep() | 
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|  | 101 | { | 
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| [cd9a59] | 102 | NOTIFY(TrajectoryChanged); | 
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| [e2373df] | 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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| [fb9eba] | 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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| [e2373df] | 110 | } | 
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|  | 111 |  | 
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| [d74077] | 112 | const element *AtomInfo::getType() const | 
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|  | 113 | { | 
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| [35a25a] | 114 | const element *elem = World::getInstance().getPeriode()->FindElement(AtomicElement); | 
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|  | 115 | return elem; | 
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| [d74077] | 116 | } | 
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|  | 117 |  | 
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| [08a0f52] | 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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| [d74077] | 129 | const double& AtomInfo::operator[](size_t i) const | 
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|  | 130 | { | 
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| [1b558c] | 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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| [d74077] | 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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| [1b558c] | 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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| [d74077] | 145 | } | 
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|  | 146 |  | 
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| [6b020f] | 147 | const double& AtomInfo::atStep(size_t i, unsigned int _step) const | 
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| [056e70] | 148 | { | 
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|  | 149 | ASSERT(AtomicPosition.size() > _step, | 
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| [1b558c] | 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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| [056e70] | 153 | return AtomicPosition[_step].at(i); | 
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|  | 154 | } | 
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|  | 155 |  | 
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| [d74077] | 156 | void AtomInfo::set(size_t i, const double value) | 
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|  | 157 | { | 
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| [7188b1] | 158 | OBSERVE; | 
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|  | 159 | NOTIFY(AtomObservable::PositionChanged); | 
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| [1b558c] | 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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| [d74077] | 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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| [1b558c] | 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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| [f16a4b] | 174 | } | 
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|  | 175 |  | 
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| [6b020f] | 176 | const Vector& AtomInfo::getPositionAtStep(const unsigned int _step) const | 
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| [6625c3] | 177 | { | 
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|  | 178 | ASSERT(_step < AtomicPosition.size(), | 
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| [1b558c] | 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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| [6625c3] | 182 | return AtomicPosition[_step]; | 
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|  | 183 | } | 
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|  | 184 |  | 
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| [7188b1] | 185 | void AtomInfo::setType(const element* _type) | 
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|  | 186 | { | 
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| [ed26ae] | 187 | if (_type->getAtomicNumber() != AtomicElement) { | 
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| [35a25a] | 188 | OBSERVE; | 
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|  | 189 | NOTIFY(AtomObservable::ElementChanged); | 
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| [ed26ae] | 190 | AtomicElement = _type->getAtomicNumber(); | 
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| [35a25a] | 191 | } | 
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| [f16a4b] | 192 | } | 
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|  | 193 |  | 
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| [7188b1] | 194 | void AtomInfo::setType(const int Z) | 
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|  | 195 | { | 
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| [ead4e6] | 196 | const element *elem = World::getInstance().getPeriode()->FindElement(Z); | 
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| [35a25a] | 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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| [f16a4b] | 202 | } | 
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| [d74077] | 203 |  | 
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| [056e70] | 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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| [bce72c] | 208 |  | 
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| [056e70] | 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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| [6625c3] | 215 |  | 
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| [bce72c] | 216 | const Vector& AtomInfo::getAtomicVelocity() const | 
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|  | 217 | { | 
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| [056e70] | 218 | ASSERT(AtomicVelocity.size() > 0, | 
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| [1b558c] | 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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| [bce72c] | 223 | } | 
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|  | 224 |  | 
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| [6b020f] | 225 | const Vector& AtomInfo::getAtomicVelocityAtStep(const unsigned int _step) const | 
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| [6625c3] | 226 | { | 
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|  | 227 | ASSERT(_step < AtomicVelocity.size(), | 
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| [1b558c] | 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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| [6625c3] | 231 | return AtomicVelocity[_step]; | 
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|  | 232 | } | 
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|  | 233 |  | 
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| [bce72c] | 234 | void AtomInfo::setAtomicVelocity(const Vector &_newvelocity) | 
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|  | 235 | { | 
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| [7188b1] | 236 | OBSERVE; | 
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|  | 237 | NOTIFY(AtomObservable::VelocityChanged); | 
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| [1b558c] | 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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| [bce72c] | 243 | } | 
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|  | 244 |  | 
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| [6b020f] | 245 | void AtomInfo::setAtomicVelocityAtStep(const unsigned int _step, const Vector &_newvelocity) | 
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| [6625c3] | 246 | { | 
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| [7188b1] | 247 | OBSERVE; | 
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|  | 248 | if (WorldTime::getTime() == _step) | 
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|  | 249 | NOTIFY(AtomObservable::VelocityChanged); | 
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| [1b558c] | 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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| [6625c3] | 256 | AtomicVelocity[_step] = _newvelocity; | 
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| [1b558c] | 257 | } else if (_step == size) { | 
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| [e2373df] | 258 | UpdateSteps(); | 
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|  | 259 | AtomicVelocity[_step] = _newvelocity; | 
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| [6625c3] | 260 | } | 
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|  | 261 | } | 
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|  | 262 |  | 
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| [bce72c] | 263 | const Vector& AtomInfo::getAtomicForce() const | 
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|  | 264 | { | 
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| [1b558c] | 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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| [bce72c] | 270 | } | 
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|  | 271 |  | 
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| [6b020f] | 272 | const Vector& AtomInfo::getAtomicForceAtStep(const unsigned int _step) const | 
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| [6625c3] | 273 | { | 
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|  | 274 | ASSERT(_step < AtomicForce.size(), | 
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| [1b558c] | 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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| [6625c3] | 278 | return AtomicForce[_step]; | 
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|  | 279 | } | 
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|  | 280 |  | 
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| [bce72c] | 281 | void AtomInfo::setAtomicForce(const Vector &_newforce) | 
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|  | 282 | { | 
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| [7188b1] | 283 | OBSERVE; | 
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| [bcb593] | 284 | NOTIFY(AtomObservable::ForceChanged); | 
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| [1b558c] | 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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| [bce72c] | 290 | } | 
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|  | 291 |  | 
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| [6b020f] | 292 | void AtomInfo::setAtomicForceAtStep(const unsigned int _step, const Vector &_newforce) | 
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| [6625c3] | 293 | { | 
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| [7188b1] | 294 | OBSERVE; | 
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|  | 295 | if (WorldTime::getTime() == _step) | 
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| [bcb593] | 296 | NOTIFY(AtomObservable::ForceChanged); | 
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| [6b020f] | 297 | const unsigned int size = AtomicForce.size(); | 
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| [056e70] | 298 | ASSERT(_step <= size, | 
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| [1b558c] | 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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| [056e70] | 302 | if(_step < size) { | 
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| [6625c3] | 303 | AtomicForce[_step] = _newforce; | 
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| [056e70] | 304 | } else if (_step == size) { | 
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| [e2373df] | 305 | UpdateSteps(); | 
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|  | 306 | AtomicForce[_step] = _newforce; | 
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| [6625c3] | 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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| [7188b1] | 317 | OBSERVE; | 
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|  | 318 | NOTIFY(AtomObservable::PropertyChanged); | 
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| [6625c3] | 319 | FixedIon = _fixedion; | 
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|  | 320 | } | 
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|  | 321 |  | 
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| [d74077] | 322 | void AtomInfo::setPosition(const Vector& _vector) | 
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|  | 323 | { | 
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| [7188b1] | 324 | OBSERVE; | 
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|  | 325 | NOTIFY(AtomObservable::PositionChanged); | 
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| [1b558c] | 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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| [d74077] | 331 | //cout << "AtomInfo::setPosition: " << getType()->symbol << " at " << getPosition() << endl; | 
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|  | 332 | } | 
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|  | 333 |  | 
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| [6b020f] | 334 | void AtomInfo::setPositionAtStep(unsigned int _step, const Vector& _vector) | 
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| [6625c3] | 335 | { | 
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| [7188b1] | 336 | OBSERVE; | 
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|  | 337 | if (WorldTime::getTime() == _step) | 
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|  | 338 | NOTIFY(AtomObservable::PositionChanged); | 
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| [1b558c] | 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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| [6625c3] | 345 | AtomicPosition[_step] = _vector; | 
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| [1b558c] | 346 | } else if (_step == size) { | 
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| [e2373df] | 347 | UpdateSteps(); | 
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|  | 348 | AtomicPosition[_step] = _vector; | 
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| [6625c3] | 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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| [d74077] | 353 | const VectorInterface& AtomInfo::operator+=(const Vector& b) | 
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|  | 354 | { | 
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| [7188b1] | 355 | OBSERVE; | 
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|  | 356 | NOTIFY(AtomObservable::PositionChanged); | 
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| [1b558c] | 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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| [d74077] | 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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| [7188b1] | 367 | OBSERVE; | 
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|  | 368 | NOTIFY(AtomObservable::PositionChanged); | 
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| [1b558c] | 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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| [d74077] | 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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| [1b558c] | 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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| [d74077] | 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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| [1b558c] | 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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| [d74077] | 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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| [1b558c] | 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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| [d74077] | 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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| [1b558c] | 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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| [d74077] | 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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| [1b558c] | 419 | ASSERT(WorldTime::getTime() < AtomicPosition.size(), | 
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|  | 420 | "AtomInfo::distance() - Access out of range: " | 
|---|
|  | 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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| [d74077] | 424 | } | 
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|  | 425 |  | 
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|  | 426 | double AtomInfo::DistanceSquared(const VectorInterface &_atom) const | 
|---|
|  | 427 | { | 
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| [1b558c] | 428 | ASSERT(WorldTime::getTime() < AtomicPosition.size(), | 
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|  | 429 | "AtomInfo::DistanceSquared() - Access out of range: " | 
|---|
|  | 430 | +toString(WorldTime::getTime()) | 
|---|
|  | 431 | +" not in [0,"+toString(AtomicPosition.size())+")."); | 
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|  | 432 | return _atom.DistanceSquared(AtomicPosition[WorldTime::getTime()]); | 
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| [d74077] | 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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| [7188b1] | 437 | OBSERVE; | 
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|  | 438 | NOTIFY(AtomObservable::PositionChanged); | 
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| [1b558c] | 439 | ASSERT(WorldTime::getTime() < AtomicPosition.size(), | 
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|  | 440 | "AtomInfo::operator=() - Access out of range: " | 
|---|
|  | 441 | +toString(WorldTime::getTime()) | 
|---|
|  | 442 | +" not in [0,"+toString(AtomicPosition.size())+")."); | 
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|  | 443 | AtomicPosition[WorldTime::getTime()] = _vector; | 
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| [d74077] | 444 | return *this; | 
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|  | 445 | } | 
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|  | 446 |  | 
|---|
|  | 447 | void AtomInfo::ScaleAll(const double *factor) | 
|---|
|  | 448 | { | 
|---|
| [7188b1] | 449 | OBSERVE; | 
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|  | 450 | NOTIFY(AtomObservable::PositionChanged); | 
|---|
| [1b558c] | 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); | 
|---|
| [d74077] | 456 | } | 
|---|
|  | 457 |  | 
|---|
|  | 458 | void AtomInfo::ScaleAll(const Vector &factor) | 
|---|
|  | 459 | { | 
|---|
| [7188b1] | 460 | OBSERVE; | 
|---|
|  | 461 | NOTIFY(AtomObservable::PositionChanged); | 
|---|
| [1b558c] | 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); | 
|---|
| [d74077] | 467 | } | 
|---|
|  | 468 |  | 
|---|
|  | 469 | void AtomInfo::Scale(const double factor) | 
|---|
|  | 470 | { | 
|---|
| [7188b1] | 471 | OBSERVE; | 
|---|
|  | 472 | NOTIFY(AtomObservable::PositionChanged); | 
|---|
| [1b558c] | 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); | 
|---|
| [d74077] | 478 | } | 
|---|
|  | 479 |  | 
|---|
|  | 480 | void AtomInfo::Zero() | 
|---|
|  | 481 | { | 
|---|
| [7188b1] | 482 | OBSERVE; | 
|---|
|  | 483 | NOTIFY(AtomObservable::PositionChanged); | 
|---|
| [1b558c] | 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(); | 
|---|
| [d74077] | 489 | } | 
|---|
|  | 490 |  | 
|---|
|  | 491 | void AtomInfo::One(const double one) | 
|---|
|  | 492 | { | 
|---|
| [7188b1] | 493 | OBSERVE; | 
|---|
|  | 494 | NOTIFY(AtomObservable::PositionChanged); | 
|---|
| [1b558c] | 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); | 
|---|
| [d74077] | 500 | } | 
|---|
|  | 501 |  | 
|---|
|  | 502 | void AtomInfo::LinearCombinationOfVectors(const Vector &x1, const Vector &x2, const Vector &x3, const double * const factors) | 
|---|
|  | 503 | { | 
|---|
| [7188b1] | 504 | OBSERVE; | 
|---|
|  | 505 | NOTIFY(AtomObservable::PositionChanged); | 
|---|
| [1b558c] | 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); | 
|---|
| [d74077] | 511 | } | 
|---|
|  | 512 |  | 
|---|
| [6625c3] | 513 | /** | 
|---|
|  | 514 | *  returns the kinetic energy of this atom at a given time step | 
|---|
|  | 515 | */ | 
|---|
| [7188b1] | 516 | double AtomInfo::getKineticEnergy(const unsigned int _step) const | 
|---|
|  | 517 | { | 
|---|
| [056e70] | 518 | ASSERT(_step < AtomicPosition.size(), | 
|---|
| [1b558c] | 519 | "AtomInfo::getKineticEnergy() - Access out of range: " | 
|---|
|  | 520 | +toString(WorldTime::getTime()) | 
|---|
|  | 521 | +" not in [0,"+toString(AtomicPosition.size())+")."); | 
|---|
| [056e70] | 522 | return getMass() * AtomicVelocity[_step].NormSquared(); | 
|---|
| [6625c3] | 523 | } | 
|---|
|  | 524 |  | 
|---|
| [7188b1] | 525 | Vector AtomInfo::getMomentum(const unsigned int _step) const | 
|---|
|  | 526 | { | 
|---|
| [056e70] | 527 | ASSERT(_step < AtomicPosition.size(), | 
|---|
| [1b558c] | 528 | "AtomInfo::getMomentum() - Access out of range: " | 
|---|
|  | 529 | +toString(WorldTime::getTime()) | 
|---|
|  | 530 | +" not in [0,"+toString(AtomicPosition.size())+")."); | 
|---|
| [056e70] | 531 | return getMass()*AtomicVelocity[_step]; | 
|---|
| [6625c3] | 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 | { | 
|---|
| [e2373df] | 540 | for (;AtomicPosition.size() <= (unsigned int)(MaxSteps);) | 
|---|
|  | 541 | UpdateSteps(); | 
|---|
|  | 542 | } | 
|---|
| [6625c3] | 543 |  | 
|---|
|  | 544 | size_t AtomInfo::getTrajectorySize() const | 
|---|
|  | 545 | { | 
|---|
|  | 546 | return AtomicPosition.size(); | 
|---|
|  | 547 | } | 
|---|
|  | 548 |  | 
|---|
| [35a25a] | 549 | double AtomInfo::getMass() const | 
|---|
|  | 550 | { | 
|---|
|  | 551 | return getType()->getMass(); | 
|---|
| [6625c3] | 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 | */ | 
|---|
| [6b020f] | 558 | void AtomInfo::CopyStepOnStep(const unsigned int dest, const unsigned int src) | 
|---|
| [6625c3] | 559 | { | 
|---|
|  | 560 | if (dest == src)  // self assignment check | 
|---|
|  | 561 | return; | 
|---|
|  | 562 |  | 
|---|
| [7188b1] | 563 | if (WorldTime::getTime() == dest){ | 
|---|
|  | 564 | NOTIFY(AtomObservable::PositionChanged); | 
|---|
|  | 565 | NOTIFY(AtomObservable::VelocityChanged); | 
|---|
|  | 566 | NOTIFY(AtomObservable::ForceChanged); | 
|---|
|  | 567 | } | 
|---|
|  | 568 |  | 
|---|
| [6625c3] | 569 | ASSERT(dest < AtomicPosition.size(), | 
|---|
| [1b558c] | 570 | "AtomInfo::CopyStepOnStep() - destination outside of current trajectory array: " | 
|---|
|  | 571 | +toString(dest) | 
|---|
|  | 572 | +" not in [0,"+toString(AtomicPosition.size())+")."); | 
|---|
| [6625c3] | 573 | ASSERT(src < AtomicPosition.size(), | 
|---|
| [1b558c] | 574 | "AtomInfo::CopyStepOnStep() - source outside of current trajectory array: " | 
|---|
|  | 575 | +toString(src) | 
|---|
|  | 576 | +" not in [0,"+toString(AtomicPosition.size())+")."); | 
|---|
| [6625c3] | 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 |  | 
|---|
| [bcb593] | 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 | * | 
|---|
| [6625c3] | 589 | * \param NextStep index of sequential step to set | 
|---|
| [435065] | 590 | * \param Deltat time step width | 
|---|
|  | 591 | * \param IsAngstroem whether the force's underlying unit of length is angstroem or bohr radii | 
|---|
| [6625c3] | 592 | */ | 
|---|
| [bcb593] | 593 | void AtomInfo::VelocityVerletUpdateX(int nr, const unsigned int NextStep, double Deltat, bool IsAngstroem) | 
|---|
| [6625c3] | 594 | { | 
|---|
| [4882d5] | 595 | const unsigned int LastStep = NextStep == 0 ? 0 : NextStep-1; | 
|---|
|  | 596 |  | 
|---|
| [435065] | 597 | LOG(2, "INFO: Particle that currently " << *this); | 
|---|
| [bcb593] | 598 | LOG(2, "INFO: Integrating position with mass=" << getMass() << " and Deltat=" | 
|---|
| [435065] | 599 | << Deltat << " at NextStep=" << NextStep); | 
|---|
| [056e70] | 600 |  | 
|---|
|  | 601 | // update position | 
|---|
| [4882d5] | 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 = | 
|---|
| [bcb593] | 608 | LOG(4, "INFO: position with force " << getAtomicForceAtStep(LastStep) << " from last step " << tempVector); | 
|---|
| [4882d5] | 609 | setPositionAtStep(NextStep, tempVector); | 
|---|
|  | 610 | LOG(3, "INFO: Position at step " << NextStep << " set to " << tempVector); | 
|---|
|  | 611 | } | 
|---|
| [bcb593] | 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); | 
|---|
| [056e70] | 633 |  | 
|---|
| [6625c3] | 634 | // Update U | 
|---|
| [4882d5] | 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 | } | 
|---|
| [6625c3] | 644 | }; | 
|---|
|  | 645 |  | 
|---|
| [fb0b62] | 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 | //} | 
|---|
| [d74077] | 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 | { | 
|---|
| [b1a5d9] | 673 | const size_t terminalstep = a.getTrajectorySize()-1; | 
|---|
| [e34254] | 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 | } | 
|---|
| [d74077] | 683 | return ost; | 
|---|
|  | 684 | } | 
|---|
|  | 685 |  | 
|---|