| [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;
 | 
|---|
 | 351 | }
 | 
|---|
 | 352 | 
 | 
|---|
| [d74077] | 353 | const VectorInterface& AtomInfo::operator+=(const Vector& b)
 | 
|---|
 | 354 | {
 | 
|---|
| [7188b1] | 355 |   OBSERVE;
 | 
|---|
 | 356 |   NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
| [1b558c] | 357 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 358 |       "AtomInfo::operator+=() - Access out of range: "
 | 
|---|
 | 359 |       +toString(WorldTime::getTime())
 | 
|---|
 | 360 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 361 |   AtomicPosition[WorldTime::getTime()] += b;
 | 
|---|
| [d74077] | 362 |   return *this;
 | 
|---|
 | 363 | }
 | 
|---|
 | 364 | 
 | 
|---|
 | 365 | const VectorInterface& AtomInfo::operator-=(const Vector& b)
 | 
|---|
 | 366 | {
 | 
|---|
| [7188b1] | 367 |   OBSERVE;
 | 
|---|
 | 368 |   NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
| [1b558c] | 369 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 370 |       "AtomInfo::operator-=() - Access out of range: "
 | 
|---|
 | 371 |       +toString(WorldTime::getTime())
 | 
|---|
 | 372 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 373 |   AtomicPosition[WorldTime::getTime()] -= b;
 | 
|---|
| [d74077] | 374 |   return *this;
 | 
|---|
 | 375 | }
 | 
|---|
 | 376 | 
 | 
|---|
 | 377 | Vector const AtomInfo::operator+(const Vector& b) const
 | 
|---|
 | 378 | {
 | 
|---|
| [1b558c] | 379 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 380 |       "AtomInfo::operator+() - Access out of range: "
 | 
|---|
 | 381 |       +toString(WorldTime::getTime())
 | 
|---|
 | 382 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 383 |   Vector a(AtomicPosition[WorldTime::getTime()]);
 | 
|---|
| [d74077] | 384 |   a += b;
 | 
|---|
 | 385 |   return a;
 | 
|---|
 | 386 | }
 | 
|---|
 | 387 | 
 | 
|---|
 | 388 | Vector const AtomInfo::operator-(const Vector& b) const
 | 
|---|
 | 389 | {
 | 
|---|
| [1b558c] | 390 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 391 |       "AtomInfo::operator-() - Access out of range: "
 | 
|---|
 | 392 |       +toString(WorldTime::getTime())
 | 
|---|
 | 393 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 394 |   Vector a(AtomicPosition[WorldTime::getTime()]);
 | 
|---|
| [d74077] | 395 |   a -= b;
 | 
|---|
 | 396 |   return a;
 | 
|---|
 | 397 | }
 | 
|---|
 | 398 | 
 | 
|---|
 | 399 | double AtomInfo::distance(const Vector &point) const
 | 
|---|
 | 400 | {
 | 
|---|
| [1b558c] | 401 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 402 |       "AtomInfo::distance() - Access out of range: "
 | 
|---|
 | 403 |       +toString(WorldTime::getTime())
 | 
|---|
 | 404 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 405 |   return AtomicPosition[WorldTime::getTime()].distance(point);
 | 
|---|
| [d74077] | 406 | }
 | 
|---|
 | 407 | 
 | 
|---|
 | 408 | double AtomInfo::DistanceSquared(const Vector &y) const
 | 
|---|
 | 409 | {
 | 
|---|
| [1b558c] | 410 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 411 |       "AtomInfo::DistanceSquared() - Access out of range: "
 | 
|---|
 | 412 |       +toString(WorldTime::getTime())
 | 
|---|
 | 413 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 414 |   return AtomicPosition[WorldTime::getTime()].DistanceSquared(y);
 | 
|---|
| [d74077] | 415 | }
 | 
|---|
 | 416 | 
 | 
|---|
 | 417 | double AtomInfo::distance(const VectorInterface &_atom) const
 | 
|---|
 | 418 | {
 | 
|---|
| [1b558c] | 419 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 420 |       "AtomInfo::distance() - Access out of range: "
 | 
|---|
 | 421 |       +toString(WorldTime::getTime())
 | 
|---|
 | 422 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 423 |   return _atom.distance(AtomicPosition[WorldTime::getTime()]);
 | 
|---|
| [d74077] | 424 | }
 | 
|---|
 | 425 | 
 | 
|---|
 | 426 | double AtomInfo::DistanceSquared(const VectorInterface &_atom) const
 | 
|---|
 | 427 | {
 | 
|---|
| [1b558c] | 428 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 429 |       "AtomInfo::DistanceSquared() - Access out of range: "
 | 
|---|
 | 430 |       +toString(WorldTime::getTime())
 | 
|---|
 | 431 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 432 |   return _atom.DistanceSquared(AtomicPosition[WorldTime::getTime()]);
 | 
|---|
| [d74077] | 433 | }
 | 
|---|
 | 434 | 
 | 
|---|
 | 435 | VectorInterface &AtomInfo::operator=(const Vector& _vector)
 | 
|---|
 | 436 | {
 | 
|---|
| [7188b1] | 437 |   OBSERVE;
 | 
|---|
 | 438 |   NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
| [1b558c] | 439 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 440 |       "AtomInfo::operator=() - Access out of range: "
 | 
|---|
 | 441 |       +toString(WorldTime::getTime())
 | 
|---|
 | 442 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 443 |   AtomicPosition[WorldTime::getTime()] = _vector;
 | 
|---|
| [d74077] | 444 |   return *this;
 | 
|---|
 | 445 | }
 | 
|---|
 | 446 | 
 | 
|---|
 | 447 | void AtomInfo::ScaleAll(const double *factor)
 | 
|---|
 | 448 | {
 | 
|---|
| [7188b1] | 449 |   OBSERVE;
 | 
|---|
 | 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 | 
 | 
|---|