1 | /*
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2 | * Project: MoleCuilder
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3 | * Description: creates and alters molecular systems
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4 | * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
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5 | * Copyright (C) 2013 Frederik Heber. All rights reserved.
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6 | *
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7 | *
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8 | * This file is part of MoleCuilder.
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9 | *
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10 | * MoleCuilder is free software: you can redistribute it and/or modify
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11 | * it under the terms of the GNU General Public License as published by
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12 | * the Free Software Foundation, either version 2 of the License, or
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13 | * (at your option) any later version.
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14 | *
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15 | * MoleCuilder is distributed in the hope that it will be useful,
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16 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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17 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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18 | * GNU General Public License for more details.
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19 | *
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20 | * You should have received a copy of the GNU General Public License
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21 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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22 | */
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23 |
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24 | /*
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25 | * atom_bondedparticle.cpp
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26 | *
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27 | * Created on: Oct 19, 2009
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28 | * Author: heber
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29 | */
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30 |
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31 | // include config.h
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32 | #ifdef HAVE_CONFIG_H
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33 | #include <config.h>
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34 | #endif
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35 |
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36 | #include "CodePatterns/MemDebug.hpp"
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37 |
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38 | #include <algorithm>
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39 | #include <boost/bind.hpp>
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40 |
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41 | #include "atom.hpp"
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42 | #include "atom_bondedparticle.hpp"
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43 | #include "Bond/bond.hpp"
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44 | #include "CodePatterns/Assert.hpp"
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45 | #include "CodePatterns/Log.hpp"
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46 | #include "CodePatterns/Verbose.hpp"
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47 | #include "Element/element.hpp"
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48 | #include "WorldTime.hpp"
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49 |
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50 | /** Constructor of class BondedParticle.
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51 | */
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52 | BondedParticle::BondedParticle()
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53 | {
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54 | ListOfBonds.insert( std::make_pair(0, emptyList) );
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55 | };
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56 |
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57 | /** Destructor of class BondedParticle.
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58 | */
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59 | BondedParticle::~BondedParticle()
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60 | {
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61 | for(BondTrajectory_t::iterator iter = ListOfBonds.begin(); !ListOfBonds.empty();
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62 | iter = ListOfBonds.begin()) {
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63 | removeAllBonds(iter->first);
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64 | ListOfBonds.erase(iter);
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65 | }
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66 | };
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67 |
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68 | /** Outputs the current atom::AdaptiveOrder and atom::MaxOrder to \a *file.
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69 | * \param *file output stream
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70 | */
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71 | void BondedParticle::OutputOrder(ofstream *file) const
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72 | {
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73 | *file << getNr() << "\t" << (int)AdaptiveOrder << "\t" << (int)MaxOrder << endl;
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74 | //LOG(2, "Storing: " << getNr() << "\t" << (int)AdaptiveOrder << "\t" << MaxOrder << ".");
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75 | };
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76 |
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77 | /** Prints all bonds of this atom with total degree.
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78 | */
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79 | void BondedParticle::OutputBondOfAtom(std::ostream &ost) const
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80 | {
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81 | const BondList& ListOfBonds = getListOfBonds();
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82 | ost << "Atom " << getName() << "/" << getNr() << " with " << ListOfBonds.size() << " bonds: ";
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83 | int TotalDegree = 0;
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84 | for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); ++Runner) {
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85 | ost << **Runner << "\t";
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86 | TotalDegree += (*Runner)->getDegree();
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87 | }
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88 | ost << " -- TotalDegree: " << TotalDegree;
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89 | };
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90 |
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91 | /** Output of atom::Nr along each bond partner per line.
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92 | * Only bonds are printed where atom::Nr is smaller than the one of the bond partner.
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93 | * \param *AdjacencyFile output stream
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94 | */
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95 | void BondedParticle::OutputBonds(ofstream * const BondFile) const
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96 | {
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97 | const BondList& ListOfBonds = getListOfBonds();
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98 | for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
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99 | if (getNr() < (*Runner)->GetOtherAtom(this)->getNr())
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100 | *BondFile << getNr() << "\t" << (*Runner)->GetOtherAtom(this)->getNr() << "\n";
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101 | };
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102 |
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103 | /**
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104 | * Adds a bond between this bonded particle and another. Returns present instance if this
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105 | * bond already exists.
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106 | *
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107 | * @param _step time step to access
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108 | * @param bonding partner
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109 | * @return pointer to created bond or to already present bonds
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110 | */
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111 | bond::ptr BondedParticle::addBond(const unsigned int _step, BondedParticle* Partner)
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112 | {
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113 | const BondList &bondlist = getListOfBondsAtStep(_step);
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114 | for (BondList::const_iterator runner = bondlist.begin();
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115 | runner != bondlist.end();
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116 | runner++) {
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117 | if ((*runner)->Contains(Partner))
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118 | return *runner;
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119 | }
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120 |
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121 | bond::ptr newBond(new bond((atom*) this, (atom*) Partner, 1));
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122 | RegisterBond(_step, newBond);
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123 | Partner->RegisterBond(_step, newBond);
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124 |
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125 | return newBond;
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126 | }
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127 |
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128 | /**
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129 | * Adds a bond between this bonded particle and another. Returns present instance if this
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130 | * bond already exists.
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131 | *
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132 | * @param bonding partner
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133 | * @return pointer to created bond or to already present bonds
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134 | */
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135 | bond::ptr BondedParticle::addBond(BondedParticle* Partner)
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136 | {
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137 | return addBond(WorldTime::getTime(), Partner);
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138 | }
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139 |
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140 | /** Helper function to find the time step to a given bond in \a Binder.
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141 | *
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142 | * \param Binder bond to look for
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143 | * \return ListOfBonds::size() - not found, else - step containing \a Binder
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144 | */
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145 | unsigned int BondedParticle::findBondsStep(bond::ptr const Binder) const
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146 | {
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147 |
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148 | size_t _step = 0;
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149 | for (;_step < ListOfBonds.size();++_step) {
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150 | const BondList& ListOfBonds = getListOfBondsAtStep(_step);
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151 | if (std::find(ListOfBonds.begin(), ListOfBonds.end(), Binder) != ListOfBonds.end())
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152 | break;
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153 | }
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154 | return _step;
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155 | }
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156 |
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157 | /** Helper function to find the iterator to a bond at a given time \a step to
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158 | * a given bond partner in \a Partner.
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159 | *
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160 | * \param _step time step to look at
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161 | * \param Partner bond partner to look for
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162 | * \return ListOfBonds::end() - not found, else - iterator pointing \a Binder
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163 | */
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164 | BondList::const_iterator BondedParticle::findBondPartnerAtStep(
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165 | const unsigned int _step,
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166 | BondedParticle * const Partner) const
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167 | {
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168 | const BondList& ListOfBonds = getListOfBondsAtStep(_step);
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169 | BondList::const_iterator iter = std::find_if(ListOfBonds.begin(), ListOfBonds.end(),
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170 | boost::bind(
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171 | static_cast<bool (bond::*)(const ParticleInfo * const) const>(&bond::Contains),
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172 | _1,
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173 | boost::cref(Partner)));
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174 | return iter;
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175 | }
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176 |
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177 | /** Removes a bond of this atom to a given \a Partner.
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178 | *
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179 | * @param _step time step
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180 | * @param Partner bond partner
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181 | */
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182 | void BondedParticle::removeBond(const unsigned int _step, BondedParticle * const Partner)
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183 | {
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184 | BondList::const_iterator iter = findBondPartnerAtStep(_step, Partner);
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185 | if (iter != getListOfBondsAtStep(_step).end()) {
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186 | // iter becomes invalid upon first unregister,
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187 | // hence store the bond someplace else first
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188 | bond::ptr const Binder = *iter;
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189 | UnregisterBond(_step, Binder);
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190 | Partner->UnregisterBond(_step, Binder);
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191 | } else
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192 | ELOG(1, "BondedParticle::removeBond() - I cannot find the bond in between "
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193 | +toString(getName())+" and "+toString(Partner->getName())+".");
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194 | }
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195 |
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196 | /** Removes a bond of this atom to a given \a Partner.
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197 | *
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198 | * @param Partner bond partner
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199 | */
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200 | void BondedParticle::removeBond(BondedParticle * const Partner)
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201 | {
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202 | removeBond(WorldTime::getTime(), Partner);
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203 | }
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204 |
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205 | /** Removes a bond for this atom.
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206 | *
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207 | * @param Binder bond to remove
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208 | */
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209 | void BondedParticle::removeBond(bond::ptr &binder)
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210 | {
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211 | if (binder != NULL) {
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212 | atom * const Other = binder->GetOtherAtom(this);
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213 | ASSERT( Other != NULL,
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214 | "BondedParticle::removeBonds() - cannot find bond partner for "
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215 | +toString(*binder)+".");
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216 | // find bond at step
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217 | unsigned int step = findBondsStep(binder);
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218 | if (step != ListOfBonds.size()) {
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219 | UnregisterBond(step, binder);
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220 | Other->UnregisterBond(step, binder);
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221 | binder.reset();
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222 | }
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223 | }
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224 | }
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225 |
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226 | /** Removes all bonds in current timestep and their instances, too.
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227 | *
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228 | */
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229 | void BondedParticle::removeAllBonds()
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230 | {
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231 | removeAllBonds(WorldTime::getTime());
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232 | }
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233 |
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234 | /** Removes all bonds for a given \a _step and their instances, too.
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235 | *
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236 | * @param _step time step to access
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237 | */
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238 | void BondedParticle::removeAllBonds(const unsigned int _step)
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239 | {
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240 | //LOG(3,"INFO: Clearing all bonds of " << *this << ": " << ListOfBonds[_step]);
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241 | BondTrajectory_t::iterator listiter = ListOfBonds.find(_step);
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242 | if (listiter != ListOfBonds.end())
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243 | for (BondList::iterator iter = listiter->second.begin();
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244 | !listiter->second.empty();
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245 | iter = listiter->second.begin()) {
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246 | //LOG(3,"INFO: Clearing bond (" << *iter << ") " << *(*iter) << " of list " << &ListOfBonds);
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247 | atom * const Other = (*iter)->GetOtherAtom(this);
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248 | ASSERT( Other != NULL,
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249 | "BondedParticle::removeAllBonds() - cannot find bond partner for "
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250 | +toString(**iter)+".");
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251 | Other->UnregisterBond(_step, *iter);
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252 | UnregisterBond(_step, *iter);
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253 | }
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254 | }
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255 |
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256 | /** Puts a given bond into atom::ListOfBonds.
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257 | * @param _step time step to access
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258 | * \param *Binder bond to insert
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259 | */
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260 | bool BondedParticle::RegisterBond(const unsigned int _step, bond::ptr const Binder)
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261 | {
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262 | bool status = false;
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263 | if (Binder != NULL) {
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264 | OBSERVE;
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265 | if (Binder->Contains(this)) {
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266 | //LOG(3,"INFO: Registering bond "<< *Binder << " with atom " << *this << " at step " << _step);
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267 | std::pair< BondTrajectory_t::iterator, bool> inserter =
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268 | ListOfBonds.insert( std::make_pair( _step, BondList(1, Binder)) );
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269 | if (!inserter.second)
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270 | inserter.first->second.push_back(Binder);
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271 | if (WorldTime::getTime() == _step)
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272 | NOTIFY(AtomObservable::BondsAdded);
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273 | status = true;
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274 | } else {
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275 | ELOG(1, *Binder << " does not contain " << *this << ".");
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276 | }
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277 | } else {
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278 | ELOG(1, "Binder is " << Binder << ".");
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279 | }
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280 | return status;
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281 | };
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282 |
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283 | /** Removes a given bond from atom::ListOfBonds.
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284 | *
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285 | * \warning This only removes this atom not its bond partner, i.e.
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286 | * both atoms need to call this function to fully empty a bond.
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287 | *
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288 | * @param _step time step to access
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289 | * \param *Binder bond to remove
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290 | */
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291 | bool BondedParticle::UnregisterBond(const unsigned int _step, bond::ptr const Binder)
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292 | {
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293 | bool status = false;
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294 | if (Binder != NULL) {
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295 | if (Binder->Contains(this)) {
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296 | OBSERVE;
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297 | //LOG(0,"INFO: Unregistering bond "<< *Binder << " from list " << &ListOfBonds << " of atom " << *this << " at step " << step);
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298 | BondTrajectory_t::iterator listiter = ListOfBonds.find(_step);
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299 | if (listiter != ListOfBonds.end()) {
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300 | #ifndef NDEBUG
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301 | BondList::const_iterator iter =
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302 | std::find(listiter->second.begin(), listiter->second.end(), Binder);
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303 | ASSERT( iter != listiter->second.end(),
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304 | "BondedParticle::UnregisterBond() - "+toString(*Binder)+" not contained at "
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305 | +toString(_step));
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306 | #endif
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307 | Binder->removeAtom(this);
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308 | listiter->second.remove(Binder);
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309 | if (WorldTime::getTime() == _step)
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310 | NOTIFY(AtomObservable::BondsRemoved);
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311 | status = true;
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312 | }
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313 | } else {
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314 | ELOG(1, *Binder << " does not contain " << *this << ".");
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315 | }
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316 | } else {
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317 | ELOG(1, "Binder is " << Binder << ".");
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318 | }
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319 | return status;
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320 | };
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321 |
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322 | /** Removes all bonds of given \a _step with freeing memory.
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323 | *
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324 | * @param _step time step whose bonds to free
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325 | */
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326 | void BondedParticle::ClearBondsAtStep(const unsigned int _step)
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327 | {
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328 | removeAllBonds(_step);
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329 | }
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330 |
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331 | /** Searches for the time step where the given bond \a *Binder is a bond of this particle.
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332 | *
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333 | * @param Binder bond to check
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334 | * @return >=0 - first time step where bond appears, -1 - bond not present in lists
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335 | */
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336 | int BondedParticle::ContainsBondAtStep(bond::ptr Binder) const
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337 | {
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338 | int step = -1;
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339 | for(BondTrajectory_t::const_iterator listiter = ListOfBonds.begin();
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340 | listiter != ListOfBonds.end();
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341 | ++listiter) {
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342 | for (BondList::const_iterator bonditer = listiter->second.begin();
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343 | bonditer != listiter->second.end();
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344 | ++bonditer) {
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345 | if ((*bonditer) == Binder) {
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346 | step = listiter->first;
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347 | break;
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348 | }
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349 | }
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350 | if (step != -1)
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351 | break;
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352 | }
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353 |
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354 | return step;
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355 | }
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356 |
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357 | /** Counts the number of bonds weighted by bond::BondDegree.
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358 | * @param _step time step to access
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359 | * \param bonds times bond::BondDegree
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360 | */
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361 | int BondedParticle::CountBonds() const
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362 | {
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363 | int NoBonds = 0;
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364 | const BondList& ListOfBonds = getListOfBonds();
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365 | for (BondList::const_iterator Runner = ListOfBonds.begin();
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366 | Runner != ListOfBonds.end();
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367 | (++Runner))
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368 | NoBonds += (*Runner)->getDegree();
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369 | return NoBonds;
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370 | };
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371 |
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372 | /** Checks whether there is a bond between \a this atom and the given \a *BondPartner.
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373 | * @param _step time step to access
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374 | * \param *BondPartner atom to check for
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375 | * \return true - bond exists, false - bond does not exist
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376 | */
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377 | bool BondedParticle::IsBondedTo(const unsigned int _step, BondedParticle * const BondPartner) const
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378 | {
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379 | bool status = false;
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380 |
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381 | const BondList& ListOfBonds = getListOfBondsAtStep(_step);
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382 | for (BondList::const_iterator runner = ListOfBonds.begin();
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383 | runner != ListOfBonds.end();
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384 | runner++) {
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385 | status = status || ((*runner)->Contains(BondPartner));
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386 | }
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387 | return status;
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388 | };
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389 |
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390 | std::ostream & BondedParticle::operator << (std::ostream &ost) const
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391 | {
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392 | ParticleInfo::operator<<(ost);
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393 | ost << "," << getPosition();
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394 | return ost;
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395 | }
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396 |
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397 | std::ostream & operator << (std::ostream &ost, const BondedParticle &a)
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398 | {
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399 | a.ParticleInfo::operator<<(ost);
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400 | ost << "," << a.getPosition();
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401 | return ost;
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402 | }
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403 |
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