| [bcf653] | 1 | /*
 | 
|---|
 | 2 |  * Project: MoleCuilder
 | 
|---|
 | 3 |  * Description: creates and alters molecular systems
 | 
|---|
| [0aa122] | 4 |  * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
 | 
|---|
| [94d5ac6] | 5 |  * 
 | 
|---|
 | 6 |  *
 | 
|---|
 | 7 |  *   This file is part of MoleCuilder.
 | 
|---|
 | 8 |  *
 | 
|---|
 | 9 |  *    MoleCuilder is free software: you can redistribute it and/or modify
 | 
|---|
 | 10 |  *    it under the terms of the GNU General Public License as published by
 | 
|---|
 | 11 |  *    the Free Software Foundation, either version 2 of the License, or
 | 
|---|
 | 12 |  *    (at your option) any later version.
 | 
|---|
 | 13 |  *
 | 
|---|
 | 14 |  *    MoleCuilder is distributed in the hope that it will be useful,
 | 
|---|
 | 15 |  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
 | 
|---|
 | 16 |  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 | 
|---|
 | 17 |  *    GNU General Public License for more details.
 | 
|---|
 | 18 |  *
 | 
|---|
 | 19 |  *    You should have received a copy of the GNU General Public License
 | 
|---|
 | 20 |  *    along with MoleCuilder.  If not, see <http://www.gnu.org/licenses/>.
 | 
|---|
| [bcf653] | 21 |  */
 | 
|---|
 | 22 | 
 | 
|---|
| [6b919f8] | 23 | /*
 | 
|---|
 | 24 |  * atom_atominfo.cpp
 | 
|---|
 | 25 |  *
 | 
|---|
 | 26 |  *  Created on: Oct 19, 2009
 | 
|---|
 | 27 |  *      Author: heber
 | 
|---|
 | 28 |  */
 | 
|---|
 | 29 | 
 | 
|---|
| [bf3817] | 30 | // include config.h
 | 
|---|
 | 31 | #ifdef HAVE_CONFIG_H
 | 
|---|
 | 32 | #include <config.h>
 | 
|---|
 | 33 | #endif
 | 
|---|
 | 34 | 
 | 
|---|
| [ad011c] | 35 | #include "CodePatterns/MemDebug.hpp"
 | 
|---|
| [112b09] | 36 | 
 | 
|---|
| [6625c3] | 37 | #include "CodePatterns/Verbose.hpp"
 | 
|---|
| [08a0f52] | 38 | 
 | 
|---|
 | 39 | #include "atom_atominfo.hpp"
 | 
|---|
 | 40 | #include "CodePatterns/Log.hpp"
 | 
|---|
| [6625c3] | 41 | #include "config.hpp"
 | 
|---|
| [3bdb6d] | 42 | #include "Element/element.hpp"
 | 
|---|
 | 43 | #include "Element/periodentafel.hpp"
 | 
|---|
| [a9b86d] | 44 | #include "Fragmentation/ForceMatrix.hpp"
 | 
|---|
| [f16a4b] | 45 | #include "World.hpp"
 | 
|---|
| [1b558c] | 46 | #include "WorldTime.hpp"
 | 
|---|
| [6b919f8] | 47 | 
 | 
|---|
| [435065] | 48 | #include <iomanip>
 | 
|---|
 | 49 | 
 | 
|---|
| [6b919f8] | 50 | /** Constructor of class AtomInfo.
 | 
|---|
 | 51 |  */
 | 
|---|
| [97b825] | 52 | AtomInfo::AtomInfo() :
 | 
|---|
| [13c969] | 53 |   AtomicElement(0),
 | 
|---|
| [2034f3] | 54 |   FixedIon(false),
 | 
|---|
 | 55 |   charge(0.)
 | 
|---|
| [54b42e] | 56 | {
 | 
|---|
 | 57 |   AtomicPosition.reserve(1);
 | 
|---|
 | 58 |   AtomicPosition.push_back(zeroVec);
 | 
|---|
 | 59 |   AtomicVelocity.reserve(1);
 | 
|---|
 | 60 |   AtomicVelocity.push_back(zeroVec);
 | 
|---|
 | 61 |   AtomicForce.reserve(1);
 | 
|---|
 | 62 |   AtomicForce.push_back(zeroVec);
 | 
|---|
| [08a0f52] | 63 | 
 | 
|---|
| [54b42e] | 64 | };
 | 
|---|
| [d74077] | 65 | 
 | 
|---|
 | 66 | /** Copy constructor of class AtomInfo.
 | 
|---|
 | 67 |  */
 | 
|---|
| [97b825] | 68 | AtomInfo::AtomInfo(const AtomInfo &_atom) :
 | 
|---|
 | 69 |     AtomicPosition(_atom.AtomicPosition),
 | 
|---|
| [6625c3] | 70 |     AtomicElement(_atom.AtomicElement),
 | 
|---|
| [2034f3] | 71 |     FixedIon(_atom.FixedIon),
 | 
|---|
 | 72 |     charge(_atom.charge)
 | 
|---|
| [6625c3] | 73 | {
 | 
|---|
 | 74 |   AtomicVelocity.reserve(1);
 | 
|---|
 | 75 |   AtomicVelocity.push_back(zeroVec);
 | 
|---|
 | 76 |   AtomicForce.reserve(1);
 | 
|---|
 | 77 |   AtomicForce.push_back(zeroVec);
 | 
|---|
 | 78 | };
 | 
|---|
| [d74077] | 79 | 
 | 
|---|
| [97b825] | 80 | AtomInfo::AtomInfo(const VectorInterface &_v) :
 | 
|---|
| [35a25a] | 81 |     AtomicElement(-1),
 | 
|---|
| [2034f3] | 82 |     FixedIon(false),
 | 
|---|
 | 83 |     charge(0.)
 | 
|---|
| [54b42e] | 84 | {
 | 
|---|
 | 85 |   AtomicPosition[0] = _v.getPosition();
 | 
|---|
| [6625c3] | 86 |   AtomicVelocity.reserve(1);
 | 
|---|
 | 87 |   AtomicVelocity.push_back(zeroVec);
 | 
|---|
 | 88 |   AtomicForce.reserve(1);
 | 
|---|
 | 89 |   AtomicForce.push_back(zeroVec);
 | 
|---|
| [54b42e] | 90 | };
 | 
|---|
| [6b919f8] | 91 | 
 | 
|---|
 | 92 | /** Destructor of class AtomInfo.
 | 
|---|
 | 93 |  */
 | 
|---|
 | 94 | AtomInfo::~AtomInfo()
 | 
|---|
 | 95 | {
 | 
|---|
 | 96 | };
 | 
|---|
 | 97 | 
 | 
|---|
| [e2373df] | 98 | void AtomInfo::AppendTrajectoryStep()
 | 
|---|
 | 99 | {
 | 
|---|
| [cd9a59] | 100 |   NOTIFY(TrajectoryChanged);
 | 
|---|
| [e2373df] | 101 |   AtomicPosition.push_back(zeroVec);
 | 
|---|
 | 102 |   AtomicVelocity.push_back(zeroVec);
 | 
|---|
 | 103 |   AtomicForce.push_back(zeroVec);
 | 
|---|
| [fb9eba] | 104 |   LOG(5,"AtomInfo::AppendTrajectoryStep() called, size is ("
 | 
|---|
 | 105 |       << AtomicPosition.size() << ","
 | 
|---|
 | 106 |       << AtomicVelocity.size() << ","
 | 
|---|
 | 107 |       << AtomicForce.size() << ")");
 | 
|---|
| [e2373df] | 108 | }
 | 
|---|
 | 109 | 
 | 
|---|
| [d74077] | 110 | const element *AtomInfo::getType() const
 | 
|---|
 | 111 | {
 | 
|---|
| [35a25a] | 112 |   const element *elem = World::getInstance().getPeriode()->FindElement(AtomicElement);
 | 
|---|
 | 113 |   return elem;
 | 
|---|
| [d74077] | 114 | }
 | 
|---|
 | 115 | 
 | 
|---|
| [08a0f52] | 116 | const element &AtomInfo::getElement() const
 | 
|---|
 | 117 | {
 | 
|---|
 | 118 |   const element &elem = *World::getInstance().getPeriode()->FindElement(AtomicElement);
 | 
|---|
 | 119 |   return elem;
 | 
|---|
 | 120 | }
 | 
|---|
 | 121 | 
 | 
|---|
 | 122 | atomicNumber_t AtomInfo::getElementNo() const
 | 
|---|
 | 123 | {
 | 
|---|
 | 124 |   return AtomicElement;
 | 
|---|
 | 125 | }
 | 
|---|
 | 126 | 
 | 
|---|
| [d74077] | 127 | const double& AtomInfo::operator[](size_t i) const
 | 
|---|
 | 128 | {
 | 
|---|
| [1b558c] | 129 |   ASSERT(AtomicPosition.size() > WorldTime::getTime(),
 | 
|---|
 | 130 |       "AtomInfo::operator[]() - Access out of range: "
 | 
|---|
 | 131 |       +toString(WorldTime::getTime())
 | 
|---|
 | 132 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 133 |   return AtomicPosition[WorldTime::getTime()][i];
 | 
|---|
| [d74077] | 134 | }
 | 
|---|
 | 135 | 
 | 
|---|
 | 136 | const double& AtomInfo::at(size_t i) const
 | 
|---|
 | 137 | {
 | 
|---|
| [1b558c] | 138 |   ASSERT(AtomicPosition.size() > WorldTime::getTime(),
 | 
|---|
 | 139 |       "AtomInfo::at() - Access out of range: "
 | 
|---|
 | 140 |       +toString(WorldTime::getTime())
 | 
|---|
 | 141 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 142 |   return AtomicPosition[WorldTime::getTime()].at(i);
 | 
|---|
| [d74077] | 143 | }
 | 
|---|
 | 144 | 
 | 
|---|
| [6b020f] | 145 | const double& AtomInfo::atStep(size_t i, unsigned int _step) const
 | 
|---|
| [056e70] | 146 | {
 | 
|---|
 | 147 |   ASSERT(AtomicPosition.size() > _step,
 | 
|---|
| [1b558c] | 148 |       "AtomInfo::atStep() - Access out of range: "
 | 
|---|
 | 149 |       +toString(_step)
 | 
|---|
 | 150 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
| [056e70] | 151 |   return AtomicPosition[_step].at(i);
 | 
|---|
 | 152 | }
 | 
|---|
 | 153 | 
 | 
|---|
| [d74077] | 154 | void AtomInfo::set(size_t i, const double value)
 | 
|---|
 | 155 | {
 | 
|---|
| [7188b1] | 156 |   OBSERVE;
 | 
|---|
 | 157 |   NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
| [1b558c] | 158 |   ASSERT(AtomicPosition.size() > WorldTime::getTime(),
 | 
|---|
 | 159 |       "AtomInfo::set() - Access out of range: "
 | 
|---|
 | 160 |       +toString(WorldTime::getTime())
 | 
|---|
 | 161 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 162 |   AtomicPosition[WorldTime::getTime()].at(i) = value;
 | 
|---|
| [d74077] | 163 | }
 | 
|---|
 | 164 | 
 | 
|---|
 | 165 | const Vector& AtomInfo::getPosition() const
 | 
|---|
 | 166 | {
 | 
|---|
| [1b558c] | 167 |   ASSERT(AtomicPosition.size() > WorldTime::getTime(),
 | 
|---|
 | 168 |       "AtomInfo::getPosition() - Access out of range: "
 | 
|---|
 | 169 |       +toString(WorldTime::getTime())
 | 
|---|
 | 170 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 171 |   return AtomicPosition[WorldTime::getTime()];
 | 
|---|
| [f16a4b] | 172 | }
 | 
|---|
 | 173 | 
 | 
|---|
| [6b020f] | 174 | const Vector& AtomInfo::getPositionAtStep(const unsigned int _step) const
 | 
|---|
| [6625c3] | 175 | {
 | 
|---|
 | 176 |   ASSERT(_step < AtomicPosition.size(),
 | 
|---|
| [1b558c] | 177 |       "AtomInfo::getPositionAtStep() - Access out of range: "
 | 
|---|
 | 178 |       +toString(_step)
 | 
|---|
 | 179 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
| [6625c3] | 180 |   return AtomicPosition[_step];
 | 
|---|
 | 181 | }
 | 
|---|
 | 182 | 
 | 
|---|
| [7188b1] | 183 | void AtomInfo::setType(const element* _type)
 | 
|---|
 | 184 | {
 | 
|---|
| [ed26ae] | 185 |   if (_type->getAtomicNumber() != AtomicElement) {
 | 
|---|
| [35a25a] | 186 |     OBSERVE;
 | 
|---|
 | 187 |     NOTIFY(AtomObservable::ElementChanged);
 | 
|---|
| [ed26ae] | 188 |     AtomicElement = _type->getAtomicNumber();
 | 
|---|
| [35a25a] | 189 |   }
 | 
|---|
| [f16a4b] | 190 | }
 | 
|---|
 | 191 | 
 | 
|---|
| [7188b1] | 192 | void AtomInfo::setType(const int Z)
 | 
|---|
 | 193 | {
 | 
|---|
| [ead4e6] | 194 |   const element *elem = World::getInstance().getPeriode()->FindElement(Z);
 | 
|---|
| [35a25a] | 195 |   if (elem != NULL) {
 | 
|---|
 | 196 |     OBSERVE;
 | 
|---|
 | 197 |     NOTIFY(AtomObservable::ElementChanged);
 | 
|---|
 | 198 |     AtomicElement = Z;
 | 
|---|
 | 199 |   }
 | 
|---|
| [f16a4b] | 200 | }
 | 
|---|
| [d74077] | 201 | 
 | 
|---|
| [056e70] | 202 | //Vector& AtomInfo::getAtomicVelocity()
 | 
|---|
 | 203 | //{
 | 
|---|
 | 204 | //  return AtomicVelocity[0];
 | 
|---|
 | 205 | //}
 | 
|---|
| [bce72c] | 206 | 
 | 
|---|
| [056e70] | 207 | //Vector& AtomInfo::getAtomicVelocity(const int _step)
 | 
|---|
 | 208 | //{
 | 
|---|
 | 209 | //  ASSERT(_step < AtomicVelocity.size(),
 | 
|---|
 | 210 | //      "AtomInfo::getAtomicVelocity() - Access out of range.");
 | 
|---|
 | 211 | //  return AtomicVelocity[_step];
 | 
|---|
 | 212 | //}
 | 
|---|
| [6625c3] | 213 | 
 | 
|---|
| [bce72c] | 214 | const Vector& AtomInfo::getAtomicVelocity() const
 | 
|---|
 | 215 | {
 | 
|---|
| [056e70] | 216 |   ASSERT(AtomicVelocity.size() > 0,
 | 
|---|
| [1b558c] | 217 |       "AtomInfo::getAtomicVelocity() - Access out of range: "
 | 
|---|
 | 218 |       +toString(WorldTime::getTime())
 | 
|---|
 | 219 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 220 |   return AtomicVelocity[WorldTime::getTime()];
 | 
|---|
| [bce72c] | 221 | }
 | 
|---|
 | 222 | 
 | 
|---|
| [6b020f] | 223 | const Vector& AtomInfo::getAtomicVelocityAtStep(const unsigned int _step) const
 | 
|---|
| [6625c3] | 224 | {
 | 
|---|
 | 225 |   ASSERT(_step < AtomicVelocity.size(),
 | 
|---|
| [1b558c] | 226 |       "AtomInfo::getAtomicVelocity() - Access out of range: "
 | 
|---|
 | 227 |       +toString(_step)
 | 
|---|
 | 228 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
| [6625c3] | 229 |   return AtomicVelocity[_step];
 | 
|---|
 | 230 | }
 | 
|---|
 | 231 | 
 | 
|---|
| [bce72c] | 232 | void AtomInfo::setAtomicVelocity(const Vector &_newvelocity)
 | 
|---|
 | 233 | {
 | 
|---|
| [7188b1] | 234 |   OBSERVE;
 | 
|---|
 | 235 |   NOTIFY(AtomObservable::VelocityChanged);
 | 
|---|
| [1b558c] | 236 |   ASSERT(WorldTime::getTime() < AtomicVelocity.size(),
 | 
|---|
 | 237 |       "AtomInfo::setAtomicVelocity() - Access out of range: "
 | 
|---|
 | 238 |       +toString(WorldTime::getTime())
 | 
|---|
 | 239 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 240 |   AtomicVelocity[WorldTime::getTime()] = _newvelocity;
 | 
|---|
| [bce72c] | 241 | }
 | 
|---|
 | 242 | 
 | 
|---|
| [6b020f] | 243 | void AtomInfo::setAtomicVelocityAtStep(const unsigned int _step, const Vector &_newvelocity)
 | 
|---|
| [6625c3] | 244 | {
 | 
|---|
| [7188b1] | 245 |   OBSERVE;
 | 
|---|
 | 246 |   if (WorldTime::getTime() == _step)
 | 
|---|
 | 247 |     NOTIFY(AtomObservable::VelocityChanged);
 | 
|---|
| [1b558c] | 248 |   const unsigned int size = AtomicVelocity.size();
 | 
|---|
 | 249 |   ASSERT(_step <= size,
 | 
|---|
 | 250 |       "AtomInfo::setAtomicVelocityAtStep() - Access out of range: "
 | 
|---|
 | 251 |       +toString(_step)
 | 
|---|
 | 252 |       +" not in [0,"+toString(size)+"].");
 | 
|---|
 | 253 |   if(_step < size) {
 | 
|---|
| [6625c3] | 254 |     AtomicVelocity[_step] = _newvelocity;
 | 
|---|
| [1b558c] | 255 |   } else if (_step == size) {
 | 
|---|
| [e2373df] | 256 |     UpdateSteps();
 | 
|---|
 | 257 |     AtomicVelocity[_step] = _newvelocity;
 | 
|---|
| [6625c3] | 258 |   }
 | 
|---|
 | 259 | }
 | 
|---|
 | 260 | 
 | 
|---|
| [bce72c] | 261 | const Vector& AtomInfo::getAtomicForce() const
 | 
|---|
 | 262 | {
 | 
|---|
| [1b558c] | 263 |   ASSERT(WorldTime::getTime() < AtomicForce.size(),
 | 
|---|
 | 264 |       "AtomInfo::getAtomicForce() - Access out of range: "
 | 
|---|
 | 265 |       +toString(WorldTime::getTime())
 | 
|---|
 | 266 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 267 |   return AtomicForce[WorldTime::getTime()];
 | 
|---|
| [bce72c] | 268 | }
 | 
|---|
 | 269 | 
 | 
|---|
| [6b020f] | 270 | const Vector& AtomInfo::getAtomicForceAtStep(const unsigned int _step) const
 | 
|---|
| [6625c3] | 271 | {
 | 
|---|
 | 272 |   ASSERT(_step < AtomicForce.size(),
 | 
|---|
| [1b558c] | 273 |       "AtomInfo::getAtomicForce() - Access out of range: "
 | 
|---|
 | 274 |       +toString(_step)
 | 
|---|
 | 275 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
| [6625c3] | 276 |   return AtomicForce[_step];
 | 
|---|
 | 277 | }
 | 
|---|
 | 278 | 
 | 
|---|
| [bce72c] | 279 | void AtomInfo::setAtomicForce(const Vector &_newforce)
 | 
|---|
 | 280 | {
 | 
|---|
| [7188b1] | 281 |   OBSERVE;
 | 
|---|
| [bcb593] | 282 |   NOTIFY(AtomObservable::ForceChanged);
 | 
|---|
| [1b558c] | 283 |   ASSERT(WorldTime::getTime() < AtomicForce.size(),
 | 
|---|
 | 284 |       "AtomInfo::setAtomicForce() - Access out of range: "
 | 
|---|
 | 285 |       +toString(WorldTime::getTime())
 | 
|---|
 | 286 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 287 |   AtomicForce[WorldTime::getTime()] = _newforce;
 | 
|---|
| [bce72c] | 288 | }
 | 
|---|
 | 289 | 
 | 
|---|
| [6b020f] | 290 | void AtomInfo::setAtomicForceAtStep(const unsigned int _step, const Vector &_newforce)
 | 
|---|
| [6625c3] | 291 | {
 | 
|---|
| [7188b1] | 292 |   OBSERVE;
 | 
|---|
 | 293 |   if (WorldTime::getTime() == _step)
 | 
|---|
| [bcb593] | 294 |     NOTIFY(AtomObservable::ForceChanged);
 | 
|---|
| [6b020f] | 295 |   const unsigned int size = AtomicForce.size();
 | 
|---|
| [056e70] | 296 |   ASSERT(_step <= size,
 | 
|---|
| [1b558c] | 297 |       "AtomInfo::setAtomicForce() - Access out of range: "
 | 
|---|
 | 298 |       +toString(_step)
 | 
|---|
 | 299 |       +" not in [0,"+toString(AtomicPosition.size())+"].");
 | 
|---|
| [056e70] | 300 |   if(_step < size) {
 | 
|---|
| [6625c3] | 301 |     AtomicForce[_step] = _newforce;
 | 
|---|
| [056e70] | 302 |   } else if (_step == size) {
 | 
|---|
| [e2373df] | 303 |     UpdateSteps();
 | 
|---|
 | 304 |     AtomicForce[_step] = _newforce;
 | 
|---|
| [6625c3] | 305 |   }
 | 
|---|
 | 306 | }
 | 
|---|
 | 307 | 
 | 
|---|
 | 308 | bool AtomInfo::getFixedIon() const
 | 
|---|
 | 309 | {
 | 
|---|
 | 310 |   return FixedIon;
 | 
|---|
 | 311 | }
 | 
|---|
 | 312 | 
 | 
|---|
 | 313 | void AtomInfo::setFixedIon(const bool _fixedion)
 | 
|---|
 | 314 | {
 | 
|---|
| [7188b1] | 315 |   OBSERVE;
 | 
|---|
 | 316 |   NOTIFY(AtomObservable::PropertyChanged);
 | 
|---|
| [6625c3] | 317 |   FixedIon = _fixedion;
 | 
|---|
 | 318 | }
 | 
|---|
 | 319 | 
 | 
|---|
| [d74077] | 320 | void AtomInfo::setPosition(const Vector& _vector)
 | 
|---|
 | 321 | {
 | 
|---|
| [7188b1] | 322 |   OBSERVE;
 | 
|---|
 | 323 |   NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
| [1b558c] | 324 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 325 |       "AtomInfo::setPosition() - Access out of range: "
 | 
|---|
 | 326 |       +toString(WorldTime::getTime())
 | 
|---|
 | 327 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 328 |   AtomicPosition[WorldTime::getTime()] = _vector;
 | 
|---|
| [d74077] | 329 |   //cout << "AtomInfo::setPosition: " << getType()->symbol << " at " << getPosition() << endl;
 | 
|---|
 | 330 | }
 | 
|---|
 | 331 | 
 | 
|---|
| [6b020f] | 332 | void AtomInfo::setPositionAtStep(unsigned int _step, const Vector& _vector)
 | 
|---|
| [6625c3] | 333 | {
 | 
|---|
| [7188b1] | 334 |   OBSERVE;
 | 
|---|
 | 335 |   if (WorldTime::getTime() == _step)
 | 
|---|
 | 336 |     NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
| [1b558c] | 337 |   const unsigned int size = AtomicPosition.size();
 | 
|---|
 | 338 |   ASSERT(_step <= size,
 | 
|---|
 | 339 |       "AtomInfo::setPosition() - Access out of range: "
 | 
|---|
 | 340 |       +toString(_step)
 | 
|---|
 | 341 |       +" not in [0,"+toString(size)+"].");
 | 
|---|
 | 342 |   if(_step < size) {
 | 
|---|
| [6625c3] | 343 |     AtomicPosition[_step] = _vector;
 | 
|---|
| [1b558c] | 344 |   } else if (_step == size) {
 | 
|---|
| [e2373df] | 345 |     UpdateSteps();
 | 
|---|
 | 346 |     AtomicPosition[_step] = _vector;
 | 
|---|
| [6625c3] | 347 |   }
 | 
|---|
 | 348 |   //cout << "AtomInfo::setPosition: " << getType()->symbol << " at " << getPosition() << endl;
 | 
|---|
 | 349 | }
 | 
|---|
 | 350 | 
 | 
|---|
| [d74077] | 351 | const VectorInterface& AtomInfo::operator+=(const Vector& b)
 | 
|---|
 | 352 | {
 | 
|---|
| [7188b1] | 353 |   OBSERVE;
 | 
|---|
 | 354 |   NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
| [1b558c] | 355 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 356 |       "AtomInfo::operator+=() - Access out of range: "
 | 
|---|
 | 357 |       +toString(WorldTime::getTime())
 | 
|---|
 | 358 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 359 |   AtomicPosition[WorldTime::getTime()] += b;
 | 
|---|
| [d74077] | 360 |   return *this;
 | 
|---|
 | 361 | }
 | 
|---|
 | 362 | 
 | 
|---|
 | 363 | const VectorInterface& AtomInfo::operator-=(const Vector& b)
 | 
|---|
 | 364 | {
 | 
|---|
| [7188b1] | 365 |   OBSERVE;
 | 
|---|
 | 366 |   NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
| [1b558c] | 367 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 368 |       "AtomInfo::operator-=() - Access out of range: "
 | 
|---|
 | 369 |       +toString(WorldTime::getTime())
 | 
|---|
 | 370 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 371 |   AtomicPosition[WorldTime::getTime()] -= b;
 | 
|---|
| [d74077] | 372 |   return *this;
 | 
|---|
 | 373 | }
 | 
|---|
 | 374 | 
 | 
|---|
 | 375 | Vector const AtomInfo::operator+(const Vector& b) const
 | 
|---|
 | 376 | {
 | 
|---|
| [1b558c] | 377 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 378 |       "AtomInfo::operator+() - Access out of range: "
 | 
|---|
 | 379 |       +toString(WorldTime::getTime())
 | 
|---|
 | 380 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 381 |   Vector a(AtomicPosition[WorldTime::getTime()]);
 | 
|---|
| [d74077] | 382 |   a += b;
 | 
|---|
 | 383 |   return a;
 | 
|---|
 | 384 | }
 | 
|---|
 | 385 | 
 | 
|---|
 | 386 | Vector const AtomInfo::operator-(const Vector& b) const
 | 
|---|
 | 387 | {
 | 
|---|
| [1b558c] | 388 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 389 |       "AtomInfo::operator-() - Access out of range: "
 | 
|---|
 | 390 |       +toString(WorldTime::getTime())
 | 
|---|
 | 391 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 392 |   Vector a(AtomicPosition[WorldTime::getTime()]);
 | 
|---|
| [d74077] | 393 |   a -= b;
 | 
|---|
 | 394 |   return a;
 | 
|---|
 | 395 | }
 | 
|---|
 | 396 | 
 | 
|---|
 | 397 | double AtomInfo::distance(const Vector &point) const
 | 
|---|
 | 398 | {
 | 
|---|
| [1b558c] | 399 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 400 |       "AtomInfo::distance() - Access out of range: "
 | 
|---|
 | 401 |       +toString(WorldTime::getTime())
 | 
|---|
 | 402 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 403 |   return AtomicPosition[WorldTime::getTime()].distance(point);
 | 
|---|
| [d74077] | 404 | }
 | 
|---|
 | 405 | 
 | 
|---|
 | 406 | double AtomInfo::DistanceSquared(const Vector &y) const
 | 
|---|
 | 407 | {
 | 
|---|
| [1b558c] | 408 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 409 |       "AtomInfo::DistanceSquared() - Access out of range: "
 | 
|---|
 | 410 |       +toString(WorldTime::getTime())
 | 
|---|
 | 411 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 412 |   return AtomicPosition[WorldTime::getTime()].DistanceSquared(y);
 | 
|---|
| [d74077] | 413 | }
 | 
|---|
 | 414 | 
 | 
|---|
 | 415 | double AtomInfo::distance(const VectorInterface &_atom) const
 | 
|---|
 | 416 | {
 | 
|---|
| [1b558c] | 417 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 418 |       "AtomInfo::distance() - Access out of range: "
 | 
|---|
 | 419 |       +toString(WorldTime::getTime())
 | 
|---|
 | 420 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 421 |   return _atom.distance(AtomicPosition[WorldTime::getTime()]);
 | 
|---|
| [d74077] | 422 | }
 | 
|---|
 | 423 | 
 | 
|---|
 | 424 | double AtomInfo::DistanceSquared(const VectorInterface &_atom) const
 | 
|---|
 | 425 | {
 | 
|---|
| [1b558c] | 426 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 427 |       "AtomInfo::DistanceSquared() - Access out of range: "
 | 
|---|
 | 428 |       +toString(WorldTime::getTime())
 | 
|---|
 | 429 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 430 |   return _atom.DistanceSquared(AtomicPosition[WorldTime::getTime()]);
 | 
|---|
| [d74077] | 431 | }
 | 
|---|
 | 432 | 
 | 
|---|
 | 433 | VectorInterface &AtomInfo::operator=(const Vector& _vector)
 | 
|---|
 | 434 | {
 | 
|---|
| [7188b1] | 435 |   OBSERVE;
 | 
|---|
 | 436 |   NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
| [1b558c] | 437 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 438 |       "AtomInfo::operator=() - Access out of range: "
 | 
|---|
 | 439 |       +toString(WorldTime::getTime())
 | 
|---|
 | 440 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 441 |   AtomicPosition[WorldTime::getTime()] = _vector;
 | 
|---|
| [d74077] | 442 |   return *this;
 | 
|---|
 | 443 | }
 | 
|---|
 | 444 | 
 | 
|---|
 | 445 | void AtomInfo::ScaleAll(const double *factor)
 | 
|---|
 | 446 | {
 | 
|---|
| [7188b1] | 447 |   OBSERVE;
 | 
|---|
 | 448 |   NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
| [1b558c] | 449 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 450 |       "AtomInfo::ScaleAll() - Access out of range: "
 | 
|---|
 | 451 |       +toString(WorldTime::getTime())
 | 
|---|
 | 452 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 453 |   AtomicPosition[WorldTime::getTime()].ScaleAll(factor);
 | 
|---|
| [d74077] | 454 | }
 | 
|---|
 | 455 | 
 | 
|---|
 | 456 | void AtomInfo::ScaleAll(const Vector &factor)
 | 
|---|
 | 457 | {
 | 
|---|
| [7188b1] | 458 |   OBSERVE;
 | 
|---|
 | 459 |   NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
| [1b558c] | 460 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 461 |       "AtomInfo::ScaleAll() - Access out of range: "
 | 
|---|
 | 462 |       +toString(WorldTime::getTime())
 | 
|---|
 | 463 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 464 |   AtomicPosition[WorldTime::getTime()].ScaleAll(factor);
 | 
|---|
| [d74077] | 465 | }
 | 
|---|
 | 466 | 
 | 
|---|
 | 467 | void AtomInfo::Scale(const double factor)
 | 
|---|
 | 468 | {
 | 
|---|
| [7188b1] | 469 |   OBSERVE;
 | 
|---|
 | 470 |   NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
| [1b558c] | 471 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 472 |       "AtomInfo::Scale() - Access out of range: "
 | 
|---|
 | 473 |       +toString(WorldTime::getTime())
 | 
|---|
 | 474 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 475 |   AtomicPosition[WorldTime::getTime()].Scale(factor);
 | 
|---|
| [d74077] | 476 | }
 | 
|---|
 | 477 | 
 | 
|---|
 | 478 | void AtomInfo::Zero()
 | 
|---|
 | 479 | {
 | 
|---|
| [7188b1] | 480 |   OBSERVE;
 | 
|---|
 | 481 |   NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
| [1b558c] | 482 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 483 |       "AtomInfo::Zero() - Access out of range: "
 | 
|---|
 | 484 |       +toString(WorldTime::getTime())
 | 
|---|
 | 485 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 486 |   AtomicPosition[WorldTime::getTime()].Zero();
 | 
|---|
| [d74077] | 487 | }
 | 
|---|
 | 488 | 
 | 
|---|
 | 489 | void AtomInfo::One(const double one)
 | 
|---|
 | 490 | {
 | 
|---|
| [7188b1] | 491 |   OBSERVE;
 | 
|---|
 | 492 |   NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
| [1b558c] | 493 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 494 |       "AtomInfo::One() - Access out of range: "
 | 
|---|
 | 495 |       +toString(WorldTime::getTime())
 | 
|---|
 | 496 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 497 |   AtomicPosition[WorldTime::getTime()].One(one);
 | 
|---|
| [d74077] | 498 | }
 | 
|---|
 | 499 | 
 | 
|---|
 | 500 | void AtomInfo::LinearCombinationOfVectors(const Vector &x1, const Vector &x2, const Vector &x3, const double * const factors)
 | 
|---|
 | 501 | {
 | 
|---|
| [7188b1] | 502 |   OBSERVE;
 | 
|---|
 | 503 |   NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
| [1b558c] | 504 |   ASSERT(WorldTime::getTime() < AtomicPosition.size(),
 | 
|---|
 | 505 |       "AtomInfo::LinearCombinationOfVectors() - Access out of range: "
 | 
|---|
 | 506 |       +toString(WorldTime::getTime())
 | 
|---|
 | 507 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
 | 508 |   AtomicPosition[WorldTime::getTime()].LinearCombinationOfVectors(x1,x2,x3,factors);
 | 
|---|
| [d74077] | 509 | }
 | 
|---|
 | 510 | 
 | 
|---|
| [6625c3] | 511 | /**
 | 
|---|
 | 512 |  *  returns the kinetic energy of this atom at a given time step
 | 
|---|
 | 513 |  */
 | 
|---|
| [7188b1] | 514 | double AtomInfo::getKineticEnergy(const unsigned int _step) const
 | 
|---|
 | 515 | {
 | 
|---|
| [056e70] | 516 |   ASSERT(_step < AtomicPosition.size(),
 | 
|---|
| [1b558c] | 517 |       "AtomInfo::getKineticEnergy() - Access out of range: "
 | 
|---|
 | 518 |       +toString(WorldTime::getTime())
 | 
|---|
 | 519 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
| [056e70] | 520 |   return getMass() * AtomicVelocity[_step].NormSquared();
 | 
|---|
| [6625c3] | 521 | }
 | 
|---|
 | 522 | 
 | 
|---|
| [7188b1] | 523 | Vector AtomInfo::getMomentum(const unsigned int _step) const
 | 
|---|
 | 524 | {
 | 
|---|
| [056e70] | 525 |   ASSERT(_step < AtomicPosition.size(),
 | 
|---|
| [1b558c] | 526 |       "AtomInfo::getMomentum() - Access out of range: "
 | 
|---|
 | 527 |       +toString(WorldTime::getTime())
 | 
|---|
 | 528 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
| [056e70] | 529 |   return getMass()*AtomicVelocity[_step];
 | 
|---|
| [6625c3] | 530 | }
 | 
|---|
 | 531 | 
 | 
|---|
 | 532 | /** Extends the trajectory STL vector to the new size.
 | 
|---|
 | 533 |  * Does nothing if \a MaxSteps is smaller than current size.
 | 
|---|
 | 534 |  * \param MaxSteps
 | 
|---|
 | 535 |  */
 | 
|---|
 | 536 | void AtomInfo::ResizeTrajectory(size_t MaxSteps)
 | 
|---|
 | 537 | {
 | 
|---|
| [e2373df] | 538 |   for (;AtomicPosition.size() <= (unsigned int)(MaxSteps);)
 | 
|---|
 | 539 |     UpdateSteps();
 | 
|---|
 | 540 | }
 | 
|---|
| [6625c3] | 541 | 
 | 
|---|
 | 542 | size_t AtomInfo::getTrajectorySize() const
 | 
|---|
 | 543 | {
 | 
|---|
 | 544 |   return AtomicPosition.size();
 | 
|---|
 | 545 | }
 | 
|---|
 | 546 | 
 | 
|---|
| [35a25a] | 547 | double AtomInfo::getMass() const
 | 
|---|
 | 548 | {
 | 
|---|
 | 549 |   return getType()->getMass();
 | 
|---|
| [6625c3] | 550 | }
 | 
|---|
 | 551 | 
 | 
|---|
 | 552 | /** Copies a given trajectory step \a src onto another \a dest
 | 
|---|
 | 553 |  * \param dest index of destination step
 | 
|---|
 | 554 |  * \param src index of source step
 | 
|---|
 | 555 |  */
 | 
|---|
| [6b020f] | 556 | void AtomInfo::CopyStepOnStep(const unsigned int dest, const unsigned int src)
 | 
|---|
| [6625c3] | 557 | {
 | 
|---|
 | 558 |   if (dest == src)  // self assignment check
 | 
|---|
 | 559 |     return;
 | 
|---|
 | 560 | 
 | 
|---|
| [7188b1] | 561 |   if (WorldTime::getTime() == dest){
 | 
|---|
 | 562 |     NOTIFY(AtomObservable::PositionChanged);
 | 
|---|
 | 563 |     NOTIFY(AtomObservable::VelocityChanged);
 | 
|---|
 | 564 |     NOTIFY(AtomObservable::ForceChanged);
 | 
|---|
 | 565 |   }
 | 
|---|
 | 566 | 
 | 
|---|
| [6625c3] | 567 |   ASSERT(dest < AtomicPosition.size(),
 | 
|---|
| [1b558c] | 568 |       "AtomInfo::CopyStepOnStep() - destination outside of current trajectory array: "
 | 
|---|
 | 569 |       +toString(dest)
 | 
|---|
 | 570 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
| [6625c3] | 571 |   ASSERT(src < AtomicPosition.size(),
 | 
|---|
| [1b558c] | 572 |       "AtomInfo::CopyStepOnStep() - source outside of current trajectory array: "
 | 
|---|
 | 573 |       +toString(src)
 | 
|---|
 | 574 |       +" not in [0,"+toString(AtomicPosition.size())+").");
 | 
|---|
| [6625c3] | 575 |   for (int n=NDIM;n--;) {
 | 
|---|
 | 576 |     AtomicPosition.at(dest)[n] = AtomicPosition.at(src)[n];
 | 
|---|
 | 577 |     AtomicVelocity.at(dest)[n] = AtomicVelocity.at(src)[n];
 | 
|---|
 | 578 |     AtomicForce.at(dest)[n] = AtomicForce.at(src)[n];
 | 
|---|
 | 579 |   }
 | 
|---|
 | 580 | };
 | 
|---|
 | 581 | 
 | 
|---|
| [bcb593] | 582 | /** Performs a velocity verlet update of the position at \a NextStep from \a LastStep information only.
 | 
|---|
 | 583 |  *
 | 
|---|
 | 584 |  * We calculate \f$x(t + \delta t) = x(t) + v(t)* \delta t + .5 * \delta t * \delta t * F(t)/m \f$.
 | 
|---|
 | 585 |  *
 | 
|---|
 | 586 |  *
 | 
|---|
| [6625c3] | 587 |  * \param NextStep index of sequential step to set
 | 
|---|
| [435065] | 588 |  * \param Deltat time step width
 | 
|---|
 | 589 |  * \param IsAngstroem whether the force's underlying unit of length is angstroem or bohr radii
 | 
|---|
| [6625c3] | 590 |  */
 | 
|---|
| [bcb593] | 591 | void AtomInfo::VelocityVerletUpdateX(int nr, const unsigned int NextStep, double Deltat, bool IsAngstroem)
 | 
|---|
| [6625c3] | 592 | {
 | 
|---|
| [4882d5] | 593 |   const unsigned int LastStep = NextStep == 0 ? 0 : NextStep-1;
 | 
|---|
 | 594 | 
 | 
|---|
| [435065] | 595 |   LOG(2, "INFO: Particle that currently " << *this);
 | 
|---|
| [bcb593] | 596 |   LOG(2, "INFO: Integrating position with mass=" << getMass() << " and Deltat="
 | 
|---|
| [435065] | 597 |       << Deltat << " at NextStep=" << NextStep);
 | 
|---|
| [056e70] | 598 | 
 | 
|---|
 | 599 |   // update position
 | 
|---|
| [4882d5] | 600 |   {
 | 
|---|
 | 601 |     Vector tempVector = getPositionAtStep(LastStep);
 | 
|---|
 | 602 |     LOG(4, "INFO: initial position from last step " << setprecision(4) << tempVector);
 | 
|---|
 | 603 |     tempVector += Deltat*(getAtomicVelocityAtStep(LastStep));     // s(t) = s(0) + v * deltat + 1/2 a * deltat^2
 | 
|---|
 | 604 |     LOG(4, "INFO: position with velocity " << getAtomicVelocityAtStep(LastStep) << " from last step " << tempVector);
 | 
|---|
 | 605 |     tempVector += .5*Deltat*Deltat*(getAtomicForceAtStep(LastStep))*(1./getMass());     // F = m * a and s =
 | 
|---|
| [bcb593] | 606 |     LOG(4, "INFO: position with force " << getAtomicForceAtStep(LastStep) << " from last step " << tempVector);
 | 
|---|
| [4882d5] | 607 |     setPositionAtStep(NextStep, tempVector);
 | 
|---|
 | 608 |     LOG(3, "INFO: Position at step " << NextStep << " set to " << tempVector);
 | 
|---|
 | 609 |   }
 | 
|---|
| [bcb593] | 610 | };
 | 
|---|
 | 611 | 
 | 
|---|
 | 612 | /** Performs a velocity verlet update of the velocity at \a NextStep.
 | 
|---|
 | 613 |  *
 | 
|---|
 | 614 |  * \note forces at NextStep should have been calculated based on position at NextStep prior
 | 
|---|
 | 615 |  * to calling this function.
 | 
|---|
 | 616 |  *
 | 
|---|
 | 617 |  * We calculate \f$v(t) = v(t - \delta t) + \delta _t * .5 * (F(t - \delta t) + F(t))/m \f$.
 | 
|---|
 | 618 |  *
 | 
|---|
 | 619 |  * Parameters are according to those in configuration class.
 | 
|---|
 | 620 |  * \param NextStep index of sequential step to set
 | 
|---|
 | 621 |  * \param Deltat time step width
 | 
|---|
 | 622 |  * \param IsAngstroem whether the force's underlying unit of length is angstroem or bohr radii
 | 
|---|
 | 623 |  */
 | 
|---|
 | 624 | void AtomInfo::VelocityVerletUpdateU(int nr, const unsigned int NextStep, double Deltat, bool IsAngstroem)
 | 
|---|
 | 625 | {
 | 
|---|
 | 626 |   const unsigned int LastStep = NextStep == 0 ? 0 : NextStep-1;
 | 
|---|
 | 627 | 
 | 
|---|
 | 628 |   LOG(2, "INFO: Particle that currently " << *this);
 | 
|---|
 | 629 |   LOG(2, "INFO: Integrating velocity with mass=" << getMass() << " and Deltat="
 | 
|---|
 | 630 |       << Deltat << " at NextStep=" << NextStep);
 | 
|---|
| [056e70] | 631 | 
 | 
|---|
| [6625c3] | 632 |   // Update U
 | 
|---|
| [4882d5] | 633 |   {
 | 
|---|
 | 634 |     Vector tempVector = getAtomicVelocityAtStep(LastStep);
 | 
|---|
 | 635 |     LOG(4, "INFO: initial velocity from last step " << tempVector);
 | 
|---|
 | 636 |     tempVector += Deltat * .5*(getAtomicForceAtStep(LastStep)+getAtomicForceAtStep(NextStep))*(1./getMass()); // v = F/m * t
 | 
|---|
 | 637 |     LOG(4, "INFO: Velocity with force from last " << getAtomicForceAtStep(LastStep)
 | 
|---|
 | 638 |         << " and present " << getAtomicForceAtStep(NextStep) << " step " << tempVector);
 | 
|---|
 | 639 |     setAtomicVelocityAtStep(NextStep, tempVector);
 | 
|---|
 | 640 |     LOG(3, "INFO: Velocity at step " << NextStep << " set to " << tempVector);
 | 
|---|
 | 641 |   }
 | 
|---|
| [6625c3] | 642 | };
 | 
|---|
 | 643 | 
 | 
|---|
| [fb0b62] | 644 | //const AtomInfo& operator*=(AtomInfo& a, const double m)
 | 
|---|
 | 645 | //{
 | 
|---|
 | 646 | //  a.Scale(m);
 | 
|---|
 | 647 | //  return a;
 | 
|---|
 | 648 | //}
 | 
|---|
 | 649 | //
 | 
|---|
 | 650 | //AtomInfo const operator*(const AtomInfo& a, const double m)
 | 
|---|
 | 651 | //{
 | 
|---|
 | 652 | //  AtomInfo copy(a);
 | 
|---|
 | 653 | //  copy *= m;
 | 
|---|
 | 654 | //  return copy;
 | 
|---|
 | 655 | //}
 | 
|---|
 | 656 | //
 | 
|---|
 | 657 | //AtomInfo const operator*(const double m, const AtomInfo& a)
 | 
|---|
 | 658 | //{
 | 
|---|
 | 659 | //  AtomInfo copy(a);
 | 
|---|
 | 660 | //  copy *= m;
 | 
|---|
 | 661 | //  return copy;
 | 
|---|
 | 662 | //}
 | 
|---|
| [d74077] | 663 | 
 | 
|---|
 | 664 | std::ostream & AtomInfo::operator << (std::ostream &ost) const
 | 
|---|
 | 665 | {
 | 
|---|
 | 666 |   return (ost << getPosition());
 | 
|---|
 | 667 | }
 | 
|---|
 | 668 | 
 | 
|---|
 | 669 | std::ostream & operator << (std::ostream &ost, const AtomInfo &a)
 | 
|---|
 | 670 | {
 | 
|---|
| [b1a5d9] | 671 |   const size_t terminalstep = a.getTrajectorySize()-1;
 | 
|---|
| [e34254] | 672 |   if (terminalstep) {
 | 
|---|
 | 673 |     ost << "starts at "
 | 
|---|
 | 674 |         << a.getPositionAtStep(0) << " and ends at "
 | 
|---|
 | 675 |         << a.getPositionAtStep(terminalstep)
 | 
|---|
 | 676 |         << " at time step " << terminalstep;
 | 
|---|
 | 677 |   } else {
 | 
|---|
 | 678 |     ost << "is at "
 | 
|---|
 | 679 |         << a.getPositionAtStep(0) << " with a single time step only";
 | 
|---|
 | 680 |   }
 | 
|---|
| [d74077] | 681 |   return ost;
 | 
|---|
 | 682 | }
 | 
|---|
 | 683 | 
 | 
|---|