1 | /** \file MoleculeListClass.cpp
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2 | *
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3 | * Function implementations for the class MoleculeListClass.
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4 | *
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5 | */
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6 |
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7 | #include <cstring>
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8 |
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9 | #include "World.hpp"
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10 | #include "atom.hpp"
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11 | #include "bond.hpp"
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12 | #include "boundary.hpp"
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13 | #include "config.hpp"
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14 | #include "element.hpp"
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15 | #include "helpers.hpp"
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16 | #include "linkedcell.hpp"
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17 | #include "lists.hpp"
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18 | #include "log.hpp"
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19 | #include "molecule.hpp"
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20 | #include "memoryallocator.hpp"
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21 | #include "periodentafel.hpp"
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22 | #include "World.hpp"
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23 |
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24 | /*********************************** Functions for class MoleculeListClass *************************/
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25 |
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26 | /** Constructor for MoleculeListClass.
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27 | */
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28 | MoleculeListClass::MoleculeListClass(World *_world) :
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29 | world(_world)
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30 | {
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31 | // empty lists
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32 | ListOfMolecules.clear();
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33 | MaxIndex = 1;
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34 | };
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35 |
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36 | /** Destructor for MoleculeListClass.
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37 | */
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38 | MoleculeListClass::~MoleculeListClass()
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39 | {
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40 | DoLog(3) && (Log() << Verbose(3) << this << ": Freeing ListOfMolcules." << endl);
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41 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
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42 | DoLog(4) && (Log() << Verbose(4) << "ListOfMolecules: Freeing " << *ListRunner << "." << endl);
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43 | world->destroyMolecule(*ListRunner);
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44 | }
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45 | DoLog(4) && (Log() << Verbose(4) << "Freeing ListOfMolecules." << endl);
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46 | ListOfMolecules.clear(); // empty list
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47 | };
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48 |
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49 | /** Insert a new molecule into the list and set its number.
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50 | * \param *mol molecule to add to list.
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51 | * \return true - add successful
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52 | */
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53 | void MoleculeListClass::insert(molecule *mol)
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54 | {
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55 | OBSERVE;
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56 | mol->IndexNr = MaxIndex++;
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57 | ListOfMolecules.push_back(mol);
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58 | mol->signOn(this);
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59 | };
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60 |
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61 | /** Compare whether two molecules are equal.
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62 | * \param *a molecule one
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63 | * \param *n molecule two
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64 | * \return lexical value (-1, 0, +1)
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65 | */
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66 | int MolCompare(const void *a, const void *b)
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67 | {
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68 | int *aList = NULL, *bList = NULL;
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69 | int Count, Counter, aCounter, bCounter;
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70 | int flag;
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71 | atom *aWalker = NULL;
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72 | atom *bWalker = NULL;
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73 |
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74 | // sort each atom list and put the numbers into a list, then go through
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75 | //Log() << Verbose(0) << "Comparing fragment no. " << *(molecule **)a << " to " << *(molecule **)b << "." << endl;
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76 | if ((**(molecule **) a).AtomCount < (**(molecule **) b).AtomCount) {
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77 | return -1;
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78 | } else {
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79 | if ((**(molecule **) a).AtomCount > (**(molecule **) b).AtomCount)
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80 | return +1;
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81 | else {
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82 | Count = (**(molecule **) a).AtomCount;
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83 | aList = new int[Count];
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84 | bList = new int[Count];
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85 |
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86 | // fill the lists
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87 | aWalker = (**(molecule **) a).start;
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88 | bWalker = (**(molecule **) b).start;
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89 | Counter = 0;
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90 | aCounter = 0;
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91 | bCounter = 0;
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92 | while ((aWalker->next != (**(molecule **) a).end) && (bWalker->next != (**(molecule **) b).end)) {
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93 | aWalker = aWalker->next;
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94 | bWalker = bWalker->next;
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95 | if (aWalker->GetTrueFather() == NULL)
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96 | aList[Counter] = Count + (aCounter++);
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97 | else
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98 | aList[Counter] = aWalker->GetTrueFather()->nr;
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99 | if (bWalker->GetTrueFather() == NULL)
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100 | bList[Counter] = Count + (bCounter++);
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101 | else
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102 | bList[Counter] = bWalker->GetTrueFather()->nr;
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103 | Counter++;
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104 | }
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105 | // check if AtomCount was for real
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106 | flag = 0;
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107 | if ((aWalker->next == (**(molecule **) a).end) && (bWalker->next != (**(molecule **) b).end)) {
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108 | flag = -1;
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109 | } else {
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110 | if ((aWalker->next != (**(molecule **) a).end) && (bWalker->next == (**(molecule **) b).end))
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111 | flag = 1;
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112 | }
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113 | if (flag == 0) {
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114 | // sort the lists
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115 | gsl_heapsort(aList, Count, sizeof(int), CompareDoubles);
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116 | gsl_heapsort(bList, Count, sizeof(int), CompareDoubles);
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117 | // compare the lists
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118 |
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119 | flag = 0;
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120 | for (int i = 0; i < Count; i++) {
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121 | if (aList[i] < bList[i]) {
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122 | flag = -1;
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123 | } else {
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124 | if (aList[i] > bList[i])
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125 | flag = 1;
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126 | }
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127 | if (flag != 0)
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128 | break;
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129 | }
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130 | }
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131 | delete[] (aList);
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132 | delete[] (bList);
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133 | return flag;
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134 | }
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135 | }
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136 | return -1;
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137 | };
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138 |
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139 | /** Output of a list of all molecules.
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140 | * \param *out output stream
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141 | */
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142 | void MoleculeListClass::Enumerate(ostream *out)
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143 | {
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144 | atom *Walker = NULL;
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145 | periodentafel *periode = World::getInstance().getPeriode();
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146 | std::map<atomicNumber_t,unsigned int> counts;
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147 | double size=0;
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148 | Vector Origin;
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149 |
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150 | // header
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151 | (*out) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
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152 | (*out) << "-----------------------------------------------" << endl;
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153 | if (ListOfMolecules.size() == 0)
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154 | (*out) << "\tNone" << endl;
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155 | else {
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156 | Origin.Zero();
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157 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
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158 | // count atoms per element and determine size of bounding sphere
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159 | size=0.;
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160 | Walker = (*ListRunner)->start;
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161 | while (Walker->next != (*ListRunner)->end) {
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162 | Walker = Walker->next;
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163 | counts[Walker->type->getNumber()]++;
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164 | if (Walker->x.DistanceSquared(Origin) > size)
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165 | size = Walker->x.DistanceSquared(Origin);
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166 | }
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167 | // output Index, Name, number of atoms, chemical formula
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168 | (*out) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t";
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169 |
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170 | std::map<atomicNumber_t,unsigned int>::reverse_iterator iter;
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171 | for(iter=counts.rbegin(); iter!=counts.rend();++iter){
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172 | atomicNumber_t Z =(*iter).first;
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173 | (*out) << periode->FindElement(Z)->getSymbol() << (*iter).second;
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174 | }
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175 | // Center and size
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176 | (*out) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
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177 | }
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178 | }
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179 | };
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180 |
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181 | /** Returns the molecule with the given index \a index.
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182 | * \param index index of the desired molecule
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183 | * \return pointer to molecule structure, NULL if not found
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184 | */
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185 | molecule * MoleculeListClass::ReturnIndex(int index)
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186 | {
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187 | for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
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188 | if ((*ListRunner)->IndexNr == index)
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189 | return (*ListRunner);
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190 | return NULL;
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191 | };
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192 |
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193 | /** Simple merge of two molecules into one.
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194 | * \param *mol destination molecule
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195 | * \param *srcmol source molecule
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196 | * \return true - merge successful, false - merge failed (probably due to non-existant indices
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197 | */
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198 | bool MoleculeListClass::SimpleMerge(molecule *mol, molecule *srcmol)
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199 | {
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200 | if (srcmol == NULL)
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201 | return false;
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202 |
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203 | // put all molecules of src into mol
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204 | atom *Walker = srcmol->start;
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205 | atom *NextAtom = Walker->next;
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206 | while (NextAtom != srcmol->end) {
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207 | Walker = NextAtom;
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208 | NextAtom = Walker->next;
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209 | srcmol->UnlinkAtom(Walker);
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210 | mol->AddAtom(Walker);
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211 | }
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212 |
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213 | // remove src
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214 | ListOfMolecules.remove(srcmol);
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215 | World::getInstance().destroyMolecule(srcmol);
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216 | return true;
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217 | };
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218 |
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219 | /** Simple add of one molecules into another.
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220 | * \param *mol destination molecule
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221 | * \param *srcmol source molecule
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222 | * \return true - merge successful, false - merge failed (probably due to non-existant indices
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223 | */
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224 | bool MoleculeListClass::SimpleAdd(molecule *mol, molecule *srcmol)
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225 | {
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226 | if (srcmol == NULL)
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227 | return false;
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228 |
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229 | // put all molecules of src into mol
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230 | atom *Walker = srcmol->start;
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231 | atom *NextAtom = Walker->next;
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232 | while (NextAtom != srcmol->end) {
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233 | Walker = NextAtom;
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234 | NextAtom = Walker->next;
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235 | Walker = mol->AddCopyAtom(Walker);
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236 | Walker->father = Walker;
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237 | }
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238 |
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239 | return true;
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240 | };
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241 |
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242 | /** Simple merge of a given set of molecules into one.
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243 | * \param *mol destination molecule
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244 | * \param *src index of set of source molecule
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245 | * \param N number of source molecules
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246 | * \return true - merge successful, false - some merges failed (probably due to non-existant indices)
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247 | */
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248 | bool MoleculeListClass::SimpleMultiMerge(molecule *mol, int *src, int N)
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249 | {
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250 | bool status = true;
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251 | // check presence of all source molecules
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252 | for (int i=0;i<N;i++) {
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253 | molecule *srcmol = ReturnIndex(src[i]);
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254 | status = status && SimpleMerge(mol, srcmol);
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255 | }
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256 | return status;
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257 | };
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258 |
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259 | /** Simple add of a given set of molecules into one.
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260 | * \param *mol destination molecule
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261 | * \param *src index of set of source molecule
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262 | * \param N number of source molecules
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263 | * \return true - merge successful, false - some merges failed (probably due to non-existant indices)
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264 | */
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265 | bool MoleculeListClass::SimpleMultiAdd(molecule *mol, int *src, int N)
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266 | {
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267 | bool status = true;
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268 | // check presence of all source molecules
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269 | for (int i=0;i<N;i++) {
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270 | molecule *srcmol = ReturnIndex(src[i]);
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271 | status = status && SimpleAdd(mol, srcmol);
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272 | }
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273 | return status;
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274 | };
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275 |
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276 | /** Scatter merge of a given set of molecules into one.
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277 | * Scatter merge distributes the molecules in such a manner that they don't overlap.
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278 | * \param *mol destination molecule
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279 | * \param *src index of set of source molecule
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280 | * \param N number of source molecules
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281 | * \return true - merge successful, false - merge failed (probably due to non-existant indices
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282 | * \TODO find scatter center for each src molecule
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283 | */
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284 | bool MoleculeListClass::ScatterMerge(molecule *mol, int *src, int N)
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285 | {
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286 | // check presence of all source molecules
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287 | for (int i=0;i<N;i++) {
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288 | // get pointer to src molecule
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289 | molecule *srcmol = ReturnIndex(src[i]);
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290 | if (srcmol == NULL)
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291 | return false;
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292 | }
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293 | // adapt each Center
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294 | for (int i=0;i<N;i++) {
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295 | // get pointer to src molecule
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296 | molecule *srcmol = ReturnIndex(src[i]);
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297 | //srcmol->Center.Zero();
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298 | srcmol->Translate(&srcmol->Center);
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299 | }
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300 | // perform a simple multi merge
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301 | SimpleMultiMerge(mol, src, N);
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302 | return true;
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303 | };
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304 |
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305 | /** Embedding merge of a given set of molecules into one.
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306 | * Embedding merge inserts one molecule into the other.
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307 | * \param *mol destination molecule (fixed one)
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308 | * \param *srcmol source molecule (variable one, where atoms are taken from)
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309 | * \return true - merge successful, false - merge failed (probably due to non-existant indices)
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310 | * \TODO linked cell dimensions for boundary points has to be as big as inner diameter!
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311 | */
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312 | bool MoleculeListClass::EmbedMerge(molecule *mol, molecule *srcmol)
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313 | {
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314 | LinkedCell *LCList = NULL;
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315 | Tesselation *TesselStruct = NULL;
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316 | if ((srcmol == NULL) || (mol == NULL)) {
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317 | DoeLog(1) && (eLog()<< Verbose(1) << "Either fixed or variable molecule is given as NULL." << endl);
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318 | return false;
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319 | }
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320 |
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321 | // calculate envelope for *mol
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322 | LCList = new LinkedCell(mol, 8.);
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323 | FindNonConvexBorder(mol, TesselStruct, (const LinkedCell *&)LCList, 4., NULL);
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324 | if (TesselStruct == NULL) {
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325 | DoeLog(1) && (eLog()<< Verbose(1) << "Could not tesselate the fixed molecule." << endl);
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326 | return false;
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327 | }
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328 | delete(LCList);
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329 | LCList = new LinkedCell(TesselStruct, 8.); // re-create with boundary points only!
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330 |
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331 | // prepare index list for bonds
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332 | srcmol->CountAtoms();
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333 | atom ** CopyAtoms = new atom*[srcmol->AtomCount];
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334 | for(int i=0;i<srcmol->AtomCount;i++)
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335 | CopyAtoms[i] = NULL;
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336 |
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337 | // for each of the source atoms check whether we are in- or outside and add copy atom
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338 | atom *Walker = srcmol->start;
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339 | int nr=0;
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340 | while (Walker->next != srcmol->end) {
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341 | Walker = Walker->next;
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342 | DoLog(2) && (Log() << Verbose(2) << "INFO: Current Walker is " << *Walker << "." << endl);
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343 | if (!TesselStruct->IsInnerPoint(Walker->x, LCList)) {
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344 | CopyAtoms[Walker->nr] = Walker->clone();
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345 | mol->AddAtom(CopyAtoms[Walker->nr]);
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346 | nr++;
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347 | } else {
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348 | // do nothing
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349 | }
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350 | }
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351 | DoLog(1) && (Log() << Verbose(1) << nr << " of " << srcmol->AtomCount << " atoms have been merged.");
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352 |
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353 | // go through all bonds and add as well
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354 | bond *Binder = srcmol->first;
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355 | while(Binder->next != srcmol->last) {
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356 | Binder = Binder->next;
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357 | DoLog(3) && (Log() << Verbose(3) << "Adding Bond between " << *CopyAtoms[Binder->leftatom->nr] << " and " << *CopyAtoms[Binder->rightatom->nr]<< "." << endl);
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358 | mol->AddBond(CopyAtoms[Binder->leftatom->nr], CopyAtoms[Binder->rightatom->nr], Binder->BondDegree);
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359 | }
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360 | delete(LCList);
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361 | return true;
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362 | };
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363 |
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364 | /** Simple output of the pointers in ListOfMolecules.
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365 | * \param *out output stream
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366 | */
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367 | void MoleculeListClass::Output(ofstream *out)
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368 | {
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369 | DoLog(1) && (Log() << Verbose(1) << "MoleculeList: ");
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370 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
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371 | DoLog(0) && (Log() << Verbose(0) << *ListRunner << "\t");
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372 | DoLog(0) && (Log() << Verbose(0) << endl);
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373 | };
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374 |
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375 | /** Calculates necessary hydrogen correction due to unwanted interaction between saturated ones.
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376 | * If for a pair of two hydrogen atoms a and b, at least is a saturated one, and a and b are not
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377 | * bonded to the same atom, then we add for this pair a correction term constructed from a Morse
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378 | * potential function fit to QM calculations with respecting to the interatomic hydrogen distance.
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379 | * \param *out output stream for debugging
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380 | * \param *path path to file
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381 | */
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382 | bool MoleculeListClass::AddHydrogenCorrection(char *path)
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383 | {
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384 | atom *Walker = NULL;
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385 | atom *Runner = NULL;
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386 | bond *Binder = NULL;
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387 | double ***FitConstant = NULL, **correction = NULL;
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388 | int a, b;
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389 | ofstream output;
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390 | ifstream input;
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391 | string line;
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392 | stringstream zeile;
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393 | double distance;
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394 | char ParsedLine[1023];
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395 | double tmp;
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396 | char *FragmentNumber = NULL;
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397 |
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398 | DoLog(1) && (Log() << Verbose(1) << "Saving hydrogen saturation correction ... ");
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399 | // 0. parse in fit constant files that should have the same dimension as the final energy files
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400 | // 0a. find dimension of matrices with constants
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401 | line = path;
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402 | line.append("/");
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403 | line += FRAGMENTPREFIX;
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404 | line += "1";
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405 | line += FITCONSTANTSUFFIX;
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406 | input.open(line.c_str());
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407 | if (input == NULL) {
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408 | DoLog(1) && (Log() << Verbose(1) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
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409 | return false;
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410 | }
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411 | a = 0;
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412 | b = -1; // we overcount by one
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413 | while (!input.eof()) {
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414 | input.getline(ParsedLine, 1023);
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415 | zeile.str(ParsedLine);
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416 | int i = 0;
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417 | while (!zeile.eof()) {
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418 | zeile >> distance;
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419 | i++;
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420 | }
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421 | if (i > a)
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422 | a = i;
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423 | b++;
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424 | }
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425 | DoLog(0) && (Log() << Verbose(0) << "I recognized " << a << " columns and " << b << " rows, ");
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426 | input.close();
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427 |
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428 | // 0b. allocate memory for constants
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429 | FitConstant = Calloc<double**>(3, "MoleculeListClass::AddHydrogenCorrection: ***FitConstant");
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430 | for (int k = 0; k < 3; k++) {
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431 | FitConstant[k] = Calloc<double*>(a, "MoleculeListClass::AddHydrogenCorrection: **FitConstant[]");
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432 | for (int i = a; i--;) {
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433 | FitConstant[k][i] = Calloc<double>(b, "MoleculeListClass::AddHydrogenCorrection: *FitConstant[][]");
|
---|
434 | }
|
---|
435 | }
|
---|
436 | // 0c. parse in constants
|
---|
437 | for (int i = 0; i < 3; i++) {
|
---|
438 | line = path;
|
---|
439 | line.append("/");
|
---|
440 | line += FRAGMENTPREFIX;
|
---|
441 | sprintf(ParsedLine, "%d", i + 1);
|
---|
442 | line += ParsedLine;
|
---|
443 | line += FITCONSTANTSUFFIX;
|
---|
444 | input.open(line.c_str());
|
---|
445 | if (input == NULL) {
|
---|
446 | DoeLog(0) && (eLog()<< Verbose(0) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
|
---|
447 | performCriticalExit();
|
---|
448 | return false;
|
---|
449 | }
|
---|
450 | int k = 0, l;
|
---|
451 | while ((!input.eof()) && (k < b)) {
|
---|
452 | input.getline(ParsedLine, 1023);
|
---|
453 | //Log() << Verbose(0) << "Current Line: " << ParsedLine << endl;
|
---|
454 | zeile.str(ParsedLine);
|
---|
455 | zeile.clear();
|
---|
456 | l = 0;
|
---|
457 | while ((!zeile.eof()) && (l < a)) {
|
---|
458 | zeile >> FitConstant[i][l][k];
|
---|
459 | //Log() << Verbose(0) << FitConstant[i][l][k] << "\t";
|
---|
460 | l++;
|
---|
461 | }
|
---|
462 | //Log() << Verbose(0) << endl;
|
---|
463 | k++;
|
---|
464 | }
|
---|
465 | input.close();
|
---|
466 | }
|
---|
467 | for (int k = 0; k < 3; k++) {
|
---|
468 | DoLog(0) && (Log() << Verbose(0) << "Constants " << k << ":" << endl);
|
---|
469 | for (int j = 0; j < b; j++) {
|
---|
470 | for (int i = 0; i < a; i++) {
|
---|
471 | DoLog(0) && (Log() << Verbose(0) << FitConstant[k][i][j] << "\t");
|
---|
472 | }
|
---|
473 | DoLog(0) && (Log() << Verbose(0) << endl);
|
---|
474 | }
|
---|
475 | DoLog(0) && (Log() << Verbose(0) << endl);
|
---|
476 | }
|
---|
477 |
|
---|
478 | // 0d. allocate final correction matrix
|
---|
479 | correction = Calloc<double*>(a, "MoleculeListClass::AddHydrogenCorrection: **correction");
|
---|
480 | for (int i = a; i--;)
|
---|
481 | correction[i] = Calloc<double>(b, "MoleculeListClass::AddHydrogenCorrection: *correction[]");
|
---|
482 |
|
---|
483 | // 1a. go through every molecule in the list
|
---|
484 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
|
---|
485 | // 1b. zero final correction matrix
|
---|
486 | for (int k = a; k--;)
|
---|
487 | for (int j = b; j--;)
|
---|
488 | correction[k][j] = 0.;
|
---|
489 | // 2. take every hydrogen that is a saturated one
|
---|
490 | Walker = (*ListRunner)->start;
|
---|
491 | while (Walker->next != (*ListRunner)->end) {
|
---|
492 | Walker = Walker->next;
|
---|
493 | //Log() << Verbose(1) << "Walker: " << *Walker << " with first bond " << *(Walker->ListOfBonds.begin()) << "." << endl;
|
---|
494 | if ((Walker->type->Z == 1) && ((Walker->father == NULL)
|
---|
495 | || (Walker->father->type->Z != 1))) { // if it's a hydrogen
|
---|
496 | Runner = (*ListRunner)->start;
|
---|
497 | while (Runner->next != (*ListRunner)->end) {
|
---|
498 | Runner = Runner->next;
|
---|
499 | //Log() << Verbose(2) << "Runner: " << *Runner << " with first bond " << *(Walker->ListOfBonds.begin()) << "." << endl;
|
---|
500 | // 3. take every other hydrogen that is the not the first and not bound to same bonding partner
|
---|
501 | Binder = *(Runner->ListOfBonds.begin());
|
---|
502 | if ((Runner->type->Z == 1) && (Runner->nr > Walker->nr) && (Binder->GetOtherAtom(Runner) != Binder->GetOtherAtom(Walker))) { // (hydrogens have only one bonding partner!)
|
---|
503 | // 4. evaluate the morse potential for each matrix component and add up
|
---|
504 | distance = Runner->x.Distance(Walker->x);
|
---|
505 | //Log() << Verbose(0) << "Fragment " << (*ListRunner)->name << ": " << *Runner << "<= " << distance << "=>" << *Walker << ":" << endl;
|
---|
506 | for (int k = 0; k < a; k++) {
|
---|
507 | for (int j = 0; j < b; j++) {
|
---|
508 | switch (k) {
|
---|
509 | case 1:
|
---|
510 | case 7:
|
---|
511 | case 11:
|
---|
512 | tmp = pow(FitConstant[0][k][j] * (1. - exp(-FitConstant[1][k][j] * (distance - FitConstant[2][k][j]))), 2);
|
---|
513 | break;
|
---|
514 | default:
|
---|
515 | tmp = FitConstant[0][k][j] * pow(distance, FitConstant[1][k][j]) + FitConstant[2][k][j];
|
---|
516 | };
|
---|
517 | correction[k][j] -= tmp; // ground state is actually lower (disturbed by additional interaction)
|
---|
518 | //Log() << Verbose(0) << tmp << "\t";
|
---|
519 | }
|
---|
520 | //Log() << Verbose(0) << endl;
|
---|
521 | }
|
---|
522 | //Log() << Verbose(0) << endl;
|
---|
523 | }
|
---|
524 | }
|
---|
525 | }
|
---|
526 | }
|
---|
527 | // 5. write final matrix to file
|
---|
528 | line = path;
|
---|
529 | line.append("/");
|
---|
530 | line += FRAGMENTPREFIX;
|
---|
531 | FragmentNumber = FixedDigitNumber(ListOfMolecules.size(), (*ListRunner)->IndexNr);
|
---|
532 | line += FragmentNumber;
|
---|
533 | delete (FragmentNumber);
|
---|
534 | line += HCORRECTIONSUFFIX;
|
---|
535 | output.open(line.c_str());
|
---|
536 | output << "Time\t\tTotal\t\tKinetic\t\tNonLocal\tCorrelation\tExchange\tPseudo\t\tHartree\t\t-Gauss\t\tEwald\t\tIonKin\t\tETotal" << endl;
|
---|
537 | for (int j = 0; j < b; j++) {
|
---|
538 | for (int i = 0; i < a; i++)
|
---|
539 | output << correction[i][j] << "\t";
|
---|
540 | output << endl;
|
---|
541 | }
|
---|
542 | output.close();
|
---|
543 | }
|
---|
544 | line = path;
|
---|
545 | line.append("/");
|
---|
546 | line += HCORRECTIONSUFFIX;
|
---|
547 | output.open(line.c_str());
|
---|
548 | output << "Time\t\tTotal\t\tKinetic\t\tNonLocal\tCorrelation\tExchange\tPseudo\t\tHartree\t\t-Gauss\t\tEwald\t\tIonKin\t\tETotal" << endl;
|
---|
549 | for (int j = 0; j < b; j++) {
|
---|
550 | for (int i = 0; i < a; i++)
|
---|
551 | output << 0 << "\t";
|
---|
552 | output << endl;
|
---|
553 | }
|
---|
554 | output.close();
|
---|
555 | // 6. free memory of parsed matrices
|
---|
556 | for (int k = 0; k < 3; k++) {
|
---|
557 | for (int i = a; i--;) {
|
---|
558 | Free(&FitConstant[k][i]);
|
---|
559 | }
|
---|
560 | Free(&FitConstant[k]);
|
---|
561 | }
|
---|
562 | Free(&FitConstant);
|
---|
563 | DoLog(0) && (Log() << Verbose(0) << "done." << endl);
|
---|
564 | return true;
|
---|
565 | };
|
---|
566 |
|
---|
567 | /** Store force indices, i.e. the connection between the nuclear index in the total molecule config and the respective atom in fragment config.
|
---|
568 | * \param *out output stream for debugging
|
---|
569 | * \param *path path to file
|
---|
570 | * \param *SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
|
---|
571 | * \return true - file written successfully, false - writing failed
|
---|
572 | */
|
---|
573 | bool MoleculeListClass::StoreForcesFile(char *path,
|
---|
574 | int *SortIndex)
|
---|
575 | {
|
---|
576 | bool status = true;
|
---|
577 | ofstream ForcesFile;
|
---|
578 | stringstream line;
|
---|
579 | atom *Walker = NULL;
|
---|
580 | periodentafel *periode=World::getInstance().getPeriode();
|
---|
581 |
|
---|
582 | // open file for the force factors
|
---|
583 | DoLog(1) && (Log() << Verbose(1) << "Saving force factors ... ");
|
---|
584 | line << path << "/" << FRAGMENTPREFIX << FORCESFILE;
|
---|
585 | ForcesFile.open(line.str().c_str(), ios::out);
|
---|
586 | if (ForcesFile != NULL) {
|
---|
587 | //Log() << Verbose(1) << "Final AtomicForcesList: ";
|
---|
588 | //output << prefix << "Forces" << endl;
|
---|
589 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
|
---|
590 | periodentafel::const_iterator elemIter;
|
---|
591 | for(elemIter=periode->begin();elemIter!=periode->end();++elemIter){
|
---|
592 | if ((*ListRunner)->ElementsInMolecule[(*elemIter).first]) { // if this element got atoms
|
---|
593 | Walker = (*ListRunner)->start;
|
---|
594 | while (Walker->next != (*ListRunner)->end) { // go through every atom of this element
|
---|
595 | Walker = Walker->next;
|
---|
596 | if (Walker->type->getNumber() == (*elemIter).first) {
|
---|
597 | if ((Walker->GetTrueFather() != NULL) && (Walker->GetTrueFather() != Walker)) {// if there is a rea
|
---|
598 | //Log() << Verbose(0) << "Walker is " << *Walker << " with true father " << *( Walker->GetTrueFather()) << ", it
|
---|
599 | ForcesFile << SortIndex[Walker->GetTrueFather()->nr] << "\t";
|
---|
600 | } else
|
---|
601 | // otherwise a -1 to indicate an added saturation hydrogen
|
---|
602 | ForcesFile << "-1\t";
|
---|
603 | }
|
---|
604 | }
|
---|
605 | }
|
---|
606 | }
|
---|
607 | ForcesFile << endl;
|
---|
608 | }
|
---|
609 | ForcesFile.close();
|
---|
610 | DoLog(1) && (Log() << Verbose(1) << "done." << endl);
|
---|
611 | } else {
|
---|
612 | status = false;
|
---|
613 | DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
|
---|
614 | }
|
---|
615 | ForcesFile.close();
|
---|
616 |
|
---|
617 | return status;
|
---|
618 | };
|
---|
619 |
|
---|
620 | /** Writes a config file for each molecule in the given \a **FragmentList.
|
---|
621 | * \param *out output stream for debugging
|
---|
622 | * \param *configuration standard configuration to attach atoms in fragment molecule to.
|
---|
623 | * \param *SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
|
---|
624 | * \param DoPeriodic true - call ScanForPeriodicCorrection, false - don't
|
---|
625 | * \param DoCentering true - call molecule::CenterEdge(), false - don't
|
---|
626 | * \return true - success (each file was written), false - something went wrong.
|
---|
627 | */
|
---|
628 | bool MoleculeListClass::OutputConfigForListOfFragments(config *configuration, int *SortIndex)
|
---|
629 | {
|
---|
630 | ofstream outputFragment;
|
---|
631 | char FragmentName[MAXSTRINGSIZE];
|
---|
632 | char PathBackup[MAXSTRINGSIZE];
|
---|
633 | bool result = true;
|
---|
634 | bool intermediateResult = true;
|
---|
635 | atom *Walker = NULL;
|
---|
636 | Vector BoxDimension;
|
---|
637 | char *FragmentNumber = NULL;
|
---|
638 | char *path = NULL;
|
---|
639 | int FragmentCounter = 0;
|
---|
640 | ofstream output;
|
---|
641 | double cell_size_backup[6];
|
---|
642 | double * const cell_size = World::getInstance().getDomain();
|
---|
643 |
|
---|
644 | // backup cell_size
|
---|
645 | for (int i=0;i<6;i++)
|
---|
646 | cell_size_backup[i] = cell_size[i];
|
---|
647 | // store the fragments as config and as xyz
|
---|
648 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
|
---|
649 | // save default path as it is changed for each fragment
|
---|
650 | path = configuration->GetDefaultPath();
|
---|
651 | if (path != NULL)
|
---|
652 | strcpy(PathBackup, path);
|
---|
653 | else {
|
---|
654 | DoeLog(0) && (eLog()<< Verbose(0) << "OutputConfigForListOfFragments: NULL default path obtained from config!" << endl);
|
---|
655 | performCriticalExit();
|
---|
656 | }
|
---|
657 |
|
---|
658 | // correct periodic
|
---|
659 | (*ListRunner)->ScanForPeriodicCorrection();
|
---|
660 |
|
---|
661 | // output xyz file
|
---|
662 | FragmentNumber = FixedDigitNumber(ListOfMolecules.size(), FragmentCounter++);
|
---|
663 | sprintf(FragmentName, "%s/%s%s.conf.xyz", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
|
---|
664 | outputFragment.open(FragmentName, ios::out);
|
---|
665 | DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ...");
|
---|
666 | if ((intermediateResult = (*ListRunner)->OutputXYZ(&outputFragment)))
|
---|
667 | DoLog(0) && (Log() << Verbose(0) << " done." << endl);
|
---|
668 | else
|
---|
669 | DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
|
---|
670 | result = result && intermediateResult;
|
---|
671 | outputFragment.close();
|
---|
672 | outputFragment.clear();
|
---|
673 |
|
---|
674 | // list atoms in fragment for debugging
|
---|
675 | DoLog(2) && (Log() << Verbose(2) << "Contained atoms: ");
|
---|
676 | Walker = (*ListRunner)->start;
|
---|
677 | while (Walker->next != (*ListRunner)->end) {
|
---|
678 | Walker = Walker->next;
|
---|
679 | DoLog(0) && (Log() << Verbose(0) << Walker->Name << " ");
|
---|
680 | }
|
---|
681 | DoLog(0) && (Log() << Verbose(0) << endl);
|
---|
682 |
|
---|
683 | // center on edge
|
---|
684 | (*ListRunner)->CenterEdge(&BoxDimension);
|
---|
685 | (*ListRunner)->SetBoxDimension(&BoxDimension); // update Box of atoms by boundary
|
---|
686 | int j = -1;
|
---|
687 | for (int k = 0; k < NDIM; k++) {
|
---|
688 | j += k + 1;
|
---|
689 | BoxDimension[k] = 2.5 * (configuration->GetIsAngstroem() ? 1. : 1. / AtomicLengthToAngstroem);
|
---|
690 | cell_size[j] = BoxDimension[k] * 2.;
|
---|
691 | }
|
---|
692 | (*ListRunner)->Translate(&BoxDimension);
|
---|
693 |
|
---|
694 | // also calculate necessary orbitals
|
---|
695 | (*ListRunner)->CountElements(); // this is a bugfix, atoms should shoulds actually be added correctly to this fragment
|
---|
696 | (*ListRunner)->CalculateOrbitals(*configuration);
|
---|
697 |
|
---|
698 | // change path in config
|
---|
699 | //strcpy(PathBackup, configuration->configpath);
|
---|
700 | sprintf(FragmentName, "%s/%s%s/", PathBackup, FRAGMENTPREFIX, FragmentNumber);
|
---|
701 | configuration->SetDefaultPath(FragmentName);
|
---|
702 |
|
---|
703 | // and save as config
|
---|
704 | sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
|
---|
705 | DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as config ...");
|
---|
706 | if ((intermediateResult = configuration->Save(FragmentName, (*ListRunner)->elemente, (*ListRunner))))
|
---|
707 | DoLog(0) && (Log() << Verbose(0) << " done." << endl);
|
---|
708 | else
|
---|
709 | DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
|
---|
710 | result = result && intermediateResult;
|
---|
711 |
|
---|
712 | // restore old config
|
---|
713 | configuration->SetDefaultPath(PathBackup);
|
---|
714 |
|
---|
715 | // and save as mpqc input file
|
---|
716 | sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
|
---|
717 | DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ...");
|
---|
718 | if ((intermediateResult = configuration->SaveMPQC(FragmentName, (*ListRunner))))
|
---|
719 | DoLog(2) && (Log() << Verbose(2) << " done." << endl);
|
---|
720 | else
|
---|
721 | DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
|
---|
722 |
|
---|
723 | result = result && intermediateResult;
|
---|
724 | //outputFragment.close();
|
---|
725 | //outputFragment.clear();
|
---|
726 | Free(&FragmentNumber);
|
---|
727 | }
|
---|
728 | DoLog(0) && (Log() << Verbose(0) << " done." << endl);
|
---|
729 |
|
---|
730 | // printing final number
|
---|
731 | DoLog(2) && (Log() << Verbose(2) << "Final number of fragments: " << FragmentCounter << "." << endl);
|
---|
732 |
|
---|
733 | // restore cell_size
|
---|
734 | for (int i=0;i<6;i++)
|
---|
735 | cell_size[i] = cell_size_backup[i];
|
---|
736 |
|
---|
737 | return result;
|
---|
738 | };
|
---|
739 |
|
---|
740 | /** Counts the number of molecules with the molecule::ActiveFlag set.
|
---|
741 | * \return number of molecules with ActiveFlag set to true.
|
---|
742 | */
|
---|
743 | int MoleculeListClass::NumberOfActiveMolecules()
|
---|
744 | {
|
---|
745 | int count = 0;
|
---|
746 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
|
---|
747 | count += ((*ListRunner)->ActiveFlag ? 1 : 0);
|
---|
748 | return count;
|
---|
749 | };
|
---|
750 |
|
---|
751 | /** Dissects given \a *mol into connected subgraphs and inserts them as new molecules but with old atoms into \a this.
|
---|
752 | * \param *out output stream for debugging
|
---|
753 | * \param *periode periodentafel
|
---|
754 | * \param *configuration config with BondGraph
|
---|
755 | */
|
---|
756 | void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration)
|
---|
757 | {
|
---|
758 | molecule *mol = World::getInstance().createMolecule();
|
---|
759 | atom *Walker = NULL;
|
---|
760 | atom *Advancer = NULL;
|
---|
761 | bond *Binder = NULL;
|
---|
762 | bond *Stepper = NULL;
|
---|
763 | // 0. gather all atoms into single molecule
|
---|
764 | for (MoleculeList::iterator MolRunner = ListOfMolecules.begin(); !ListOfMolecules.empty(); MolRunner = ListOfMolecules.begin()) {
|
---|
765 | // shift all atoms to new molecule
|
---|
766 | Advancer = (*MolRunner)->start->next;
|
---|
767 | while (Advancer != (*MolRunner)->end) {
|
---|
768 | Walker = Advancer;
|
---|
769 | Advancer = Advancer->next;
|
---|
770 | DoLog(3) && (Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl);
|
---|
771 | unlink(Walker);
|
---|
772 | Walker->father = Walker;
|
---|
773 | mol->AddAtom(Walker); // counting starts at 1
|
---|
774 | }
|
---|
775 | // remove all bonds
|
---|
776 | Stepper = (*MolRunner)->first->next;
|
---|
777 | while (Stepper != (*MolRunner)->last) {
|
---|
778 | Binder = Stepper;
|
---|
779 | Stepper = Stepper->next;
|
---|
780 | delete(Binder);
|
---|
781 | }
|
---|
782 | // remove the molecule
|
---|
783 | World::getInstance().destroyMolecule(*MolRunner);
|
---|
784 | ListOfMolecules.erase(MolRunner);
|
---|
785 | }
|
---|
786 |
|
---|
787 | // 1. dissect the molecule into connected subgraphs
|
---|
788 | if (!configuration->BG->ConstructBondGraph(mol)) {
|
---|
789 | World::getInstance().destroyMolecule(mol);
|
---|
790 | DoeLog(1) && (eLog()<< Verbose(1) << "There are no bonds." << endl);
|
---|
791 | return;
|
---|
792 | }
|
---|
793 |
|
---|
794 | // 2. scan for connected subgraphs
|
---|
795 | MoleculeLeafClass *Subgraphs = NULL; // list of subgraphs from DFS analysis
|
---|
796 | class StackClass<bond *> *BackEdgeStack = NULL;
|
---|
797 | Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
|
---|
798 | delete(BackEdgeStack);
|
---|
799 | if ((Subgraphs == NULL) || (Subgraphs->next == NULL)) {
|
---|
800 | World::getInstance().destroyMolecule(mol);
|
---|
801 | DoeLog(1) && (eLog()<< Verbose(1) << "There are no atoms." << endl);
|
---|
802 | return;
|
---|
803 | }
|
---|
804 |
|
---|
805 | // 3. dissect (the following construct is needed to have the atoms not in the order of the DFS, but in
|
---|
806 | // the original one as parsed in)
|
---|
807 | // TODO: Optimize this, when molecules just contain pointer list of global atoms!
|
---|
808 |
|
---|
809 | // 4a. create array of molecules to fill
|
---|
810 | const int MolCount = Subgraphs->next->Count();
|
---|
811 | char number[MAXSTRINGSIZE];
|
---|
812 | molecule **molecules = Malloc<molecule *>(MolCount, "config::Load() - **molecules");
|
---|
813 | for (int i=0;i<MolCount;i++) {
|
---|
814 | molecules[i] = World::getInstance().createMolecule();
|
---|
815 | molecules[i]->ActiveFlag = true;
|
---|
816 | strncpy(molecules[i]->name, mol->name, MAXSTRINGSIZE);
|
---|
817 | if (MolCount > 1) {
|
---|
818 | sprintf(number, "-%d", i+1);
|
---|
819 | strncat(molecules[i]->name, number, MAXSTRINGSIZE - strlen(mol->name) - 1);
|
---|
820 | }
|
---|
821 | DoLog(1) && (Log() << Verbose(1) << "MolName is " << molecules[i]->name << endl);
|
---|
822 | insert(molecules[i]);
|
---|
823 | }
|
---|
824 |
|
---|
825 | // 4b. create and fill map of which atom is associated to which connected molecule (note, counting starts at 1)
|
---|
826 | int FragmentCounter = 0;
|
---|
827 | int *MolMap = Calloc<int>(mol->AtomCount, "config::Load() - *MolMap");
|
---|
828 | MoleculeLeafClass *MolecularWalker = Subgraphs;
|
---|
829 | Walker = NULL;
|
---|
830 | while (MolecularWalker->next != NULL) {
|
---|
831 | MolecularWalker = MolecularWalker->next;
|
---|
832 | Walker = MolecularWalker->Leaf->start;
|
---|
833 | while (Walker->next != MolecularWalker->Leaf->end) {
|
---|
834 | Walker = Walker->next;
|
---|
835 | MolMap[Walker->GetTrueFather()->nr] = FragmentCounter+1;
|
---|
836 | }
|
---|
837 | FragmentCounter++;
|
---|
838 | }
|
---|
839 |
|
---|
840 | // 4c. relocate atoms to new molecules and remove from Leafs
|
---|
841 | Walker = NULL;
|
---|
842 | while (mol->start->next != mol->end) {
|
---|
843 | Walker = mol->start->next;
|
---|
844 | if ((Walker->nr <0) || (Walker->nr >= mol->AtomCount)) {
|
---|
845 | DoeLog(0) && (eLog()<< Verbose(0) << "Index of atom " << *Walker << " is invalid!" << endl);
|
---|
846 | performCriticalExit();
|
---|
847 | }
|
---|
848 | FragmentCounter = MolMap[Walker->nr];
|
---|
849 | if (FragmentCounter != 0) {
|
---|
850 | DoLog(3) && (Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl);
|
---|
851 | unlink(Walker);
|
---|
852 | molecules[FragmentCounter-1]->AddAtom(Walker); // counting starts at 1
|
---|
853 | } else {
|
---|
854 | DoeLog(0) && (eLog()<< Verbose(0) << "Atom " << *Walker << " not associated to molecule!" << endl);
|
---|
855 | performCriticalExit();
|
---|
856 | }
|
---|
857 | }
|
---|
858 | // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintain their ListOfBonds, but we have to remove them from first..last list
|
---|
859 | Binder = mol->first;
|
---|
860 | while (mol->first->next != mol->last) {
|
---|
861 | Binder = mol->first->next;
|
---|
862 | Walker = Binder->leftatom;
|
---|
863 | unlink(Binder);
|
---|
864 | link(Binder,molecules[MolMap[Walker->nr]-1]->last); // counting starts at 1
|
---|
865 | }
|
---|
866 | // 4e. free Leafs
|
---|
867 | MolecularWalker = Subgraphs;
|
---|
868 | while (MolecularWalker->next != NULL) {
|
---|
869 | MolecularWalker = MolecularWalker->next;
|
---|
870 | delete(MolecularWalker->previous);
|
---|
871 | }
|
---|
872 | delete(MolecularWalker);
|
---|
873 | Free(&MolMap);
|
---|
874 | Free(&molecules);
|
---|
875 | DoLog(1) && (Log() << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl);
|
---|
876 | };
|
---|
877 |
|
---|
878 | /** Count all atoms in each molecule.
|
---|
879 | * \return number of atoms in the MoleculeListClass.
|
---|
880 | * TODO: the inner loop should be done by some (double molecule::CountAtom()) function
|
---|
881 | */
|
---|
882 | int MoleculeListClass::CountAllAtoms() const
|
---|
883 | {
|
---|
884 | atom *Walker = NULL;
|
---|
885 | int AtomNo = 0;
|
---|
886 | for (MoleculeList::const_iterator MolWalker = ListOfMolecules.begin(); MolWalker != ListOfMolecules.end(); MolWalker++) {
|
---|
887 | Walker = (*MolWalker)->start;
|
---|
888 | while (Walker->next != (*MolWalker)->end) {
|
---|
889 | Walker = Walker->next;
|
---|
890 | AtomNo++;
|
---|
891 | }
|
---|
892 | }
|
---|
893 | return AtomNo;
|
---|
894 | }
|
---|
895 |
|
---|
896 | /***********
|
---|
897 | * Methods Moved here from the menus
|
---|
898 | */
|
---|
899 |
|
---|
900 | void MoleculeListClass::flipChosen() {
|
---|
901 | int j;
|
---|
902 | Log() << Verbose(0) << "Enter index of molecule: ";
|
---|
903 | cin >> j;
|
---|
904 | for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
|
---|
905 | if ((*ListRunner)->IndexNr == j)
|
---|
906 | (*ListRunner)->ActiveFlag = !(*ListRunner)->ActiveFlag;
|
---|
907 | }
|
---|
908 |
|
---|
909 | void MoleculeListClass::createNewMolecule(periodentafel *periode) {
|
---|
910 | OBSERVE;
|
---|
911 | molecule *mol = NULL;
|
---|
912 | mol = World::getInstance().createMolecule();
|
---|
913 | insert(mol);
|
---|
914 | };
|
---|
915 |
|
---|
916 | void MoleculeListClass::loadFromXYZ(periodentafel *periode){
|
---|
917 | molecule *mol = NULL;
|
---|
918 | Vector center;
|
---|
919 | char filename[MAXSTRINGSIZE];
|
---|
920 | Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
|
---|
921 | mol = World::getInstance().createMolecule();
|
---|
922 | do {
|
---|
923 | Log() << Verbose(0) << "Enter file name: ";
|
---|
924 | cin >> filename;
|
---|
925 | } while (!mol->AddXYZFile(filename));
|
---|
926 | mol->SetNameFromFilename(filename);
|
---|
927 | // center at set box dimensions
|
---|
928 | mol->CenterEdge(¢er);
|
---|
929 | World::getInstance().getDomain()[0] = center[0];
|
---|
930 | World::getInstance().getDomain()[1] = 0;
|
---|
931 | World::getInstance().getDomain()[2] = center[1];
|
---|
932 | World::getInstance().getDomain()[3] = 0;
|
---|
933 | World::getInstance().getDomain()[4] = 0;
|
---|
934 | World::getInstance().getDomain()[5] = center[2];
|
---|
935 | insert(mol);
|
---|
936 | }
|
---|
937 |
|
---|
938 | void MoleculeListClass::setMoleculeFilename() {
|
---|
939 | char filename[MAXSTRINGSIZE];
|
---|
940 | int nr;
|
---|
941 | molecule *mol = NULL;
|
---|
942 | do {
|
---|
943 | Log() << Verbose(0) << "Enter index of molecule: ";
|
---|
944 | cin >> nr;
|
---|
945 | mol = ReturnIndex(nr);
|
---|
946 | } while (mol == NULL);
|
---|
947 | Log() << Verbose(0) << "Enter name: ";
|
---|
948 | cin >> filename;
|
---|
949 | mol->SetNameFromFilename(filename);
|
---|
950 | }
|
---|
951 |
|
---|
952 | void MoleculeListClass::parseXYZIntoMolecule(){
|
---|
953 | char filename[MAXSTRINGSIZE];
|
---|
954 | int nr;
|
---|
955 | molecule *mol = NULL;
|
---|
956 | mol = NULL;
|
---|
957 | do {
|
---|
958 | Log() << Verbose(0) << "Enter index of molecule: ";
|
---|
959 | cin >> nr;
|
---|
960 | mol = ReturnIndex(nr);
|
---|
961 | } while (mol == NULL);
|
---|
962 | Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
|
---|
963 | do {
|
---|
964 | Log() << Verbose(0) << "Enter file name: ";
|
---|
965 | cin >> filename;
|
---|
966 | } while (!mol->AddXYZFile(filename));
|
---|
967 | mol->SetNameFromFilename(filename);
|
---|
968 | };
|
---|
969 |
|
---|
970 | void MoleculeListClass::eraseMolecule(){
|
---|
971 | int nr;
|
---|
972 | molecule *mol = NULL;
|
---|
973 | Log() << Verbose(0) << "Enter index of molecule: ";
|
---|
974 | cin >> nr;
|
---|
975 | for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
|
---|
976 | if (nr == (*ListRunner)->IndexNr) {
|
---|
977 | mol = *ListRunner;
|
---|
978 | ListOfMolecules.erase(ListRunner);
|
---|
979 | World::getInstance().destroyMolecule(mol);
|
---|
980 | break;
|
---|
981 | }
|
---|
982 | };
|
---|
983 |
|
---|
984 |
|
---|
985 | /******************************************* Class MoleculeLeafClass ************************************************/
|
---|
986 |
|
---|
987 | /** Constructor for MoleculeLeafClass root leaf.
|
---|
988 | * \param *Up Leaf on upper level
|
---|
989 | * \param *PreviousLeaf NULL - We are the first leaf on this level, otherwise points to previous in list
|
---|
990 | */
|
---|
991 | //MoleculeLeafClass::MoleculeLeafClass(MoleculeLeafClass *Up = NULL, MoleculeLeafClass *Previous = NULL)
|
---|
992 | MoleculeLeafClass::MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf = NULL)
|
---|
993 | {
|
---|
994 | // if (Up != NULL)
|
---|
995 | // if (Up->DownLeaf == NULL) // are we the first down leaf for the upper leaf?
|
---|
996 | // Up->DownLeaf = this;
|
---|
997 | // UpLeaf = Up;
|
---|
998 | // DownLeaf = NULL;
|
---|
999 | Leaf = NULL;
|
---|
1000 | previous = PreviousLeaf;
|
---|
1001 | if (previous != NULL) {
|
---|
1002 | MoleculeLeafClass *Walker = previous->next;
|
---|
1003 | previous->next = this;
|
---|
1004 | next = Walker;
|
---|
1005 | } else {
|
---|
1006 | next = NULL;
|
---|
1007 | }
|
---|
1008 | };
|
---|
1009 |
|
---|
1010 | /** Destructor for MoleculeLeafClass.
|
---|
1011 | */
|
---|
1012 | MoleculeLeafClass::~MoleculeLeafClass()
|
---|
1013 | {
|
---|
1014 | // if (DownLeaf != NULL) {// drop leaves further down
|
---|
1015 | // MoleculeLeafClass *Walker = DownLeaf;
|
---|
1016 | // MoleculeLeafClass *Next;
|
---|
1017 | // do {
|
---|
1018 | // Next = Walker->NextLeaf;
|
---|
1019 | // delete(Walker);
|
---|
1020 | // Walker = Next;
|
---|
1021 | // } while (Walker != NULL);
|
---|
1022 | // // Last Walker sets DownLeaf automatically to NULL
|
---|
1023 | // }
|
---|
1024 | // remove the leaf itself
|
---|
1025 | if (Leaf != NULL) {
|
---|
1026 | World::getInstance().destroyMolecule(Leaf);
|
---|
1027 | Leaf = NULL;
|
---|
1028 | }
|
---|
1029 | // remove this Leaf from level list
|
---|
1030 | if (previous != NULL)
|
---|
1031 | previous->next = next;
|
---|
1032 | // } else { // we are first in list (connects to UpLeaf->DownLeaf)
|
---|
1033 | // if ((NextLeaf != NULL) && (NextLeaf->UpLeaf == NULL))
|
---|
1034 | // NextLeaf->UpLeaf = UpLeaf; // either null as we are top level or the upleaf of the first node
|
---|
1035 | // if (UpLeaf != NULL)
|
---|
1036 | // UpLeaf->DownLeaf = NextLeaf; // either null as we are only leaf or NextLeaf if we are just the first
|
---|
1037 | // }
|
---|
1038 | // UpLeaf = NULL;
|
---|
1039 | if (next != NULL) // are we last in list
|
---|
1040 | next->previous = previous;
|
---|
1041 | next = NULL;
|
---|
1042 | previous = NULL;
|
---|
1043 | };
|
---|
1044 |
|
---|
1045 | /** Adds \a molecule leaf to the tree.
|
---|
1046 | * \param *ptr ptr to molecule to be added
|
---|
1047 | * \param *Previous previous MoleculeLeafClass referencing level and which on the level
|
---|
1048 | * \return true - success, false - something went wrong
|
---|
1049 | */
|
---|
1050 | bool MoleculeLeafClass::AddLeaf(molecule *ptr, MoleculeLeafClass *Previous)
|
---|
1051 | {
|
---|
1052 | return false;
|
---|
1053 | };
|
---|
1054 |
|
---|
1055 | /** Fills the bond structure of this chain list subgraphs that are derived from a complete \a *reference molecule.
|
---|
1056 | * Calls this routine in each MoleculeLeafClass::next subgraph if it's not NULL.
|
---|
1057 | * \param *out output stream for debugging
|
---|
1058 | * \param *reference reference molecule with the bond structure to be copied
|
---|
1059 | * \param &FragmentCounter Counter needed to address \a **ListOfLocalAtoms
|
---|
1060 | * \param ***ListOfLocalAtoms Lookup table for each subgraph and index of each atom in \a *reference, may be NULL on start, then it is filled
|
---|
1061 | * \param FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
|
---|
1062 | * \return true - success, false - faoilure
|
---|
1063 | */
|
---|
1064 | bool MoleculeLeafClass::FillBondStructureFromReference(const molecule * const reference, int &FragmentCounter, atom ***&ListOfLocalAtoms, bool FreeList)
|
---|
1065 | {
|
---|
1066 | atom *Walker = NULL;
|
---|
1067 | atom *OtherWalker = NULL;
|
---|
1068 | atom *Father = NULL;
|
---|
1069 | bool status = true;
|
---|
1070 | int AtomNo;
|
---|
1071 |
|
---|
1072 | DoLog(1) && (Log() << Verbose(1) << "Begin of FillBondStructureFromReference." << endl);
|
---|
1073 | // fill ListOfLocalAtoms if NULL was given
|
---|
1074 | if (!FillListOfLocalAtoms(ListOfLocalAtoms, FragmentCounter, reference->AtomCount, FreeList)) {
|
---|
1075 | DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
|
---|
1076 | return false;
|
---|
1077 | }
|
---|
1078 |
|
---|
1079 | if (status) {
|
---|
1080 | DoLog(1) && (Log() << Verbose(1) << "Creating adjacency list for subgraph " << Leaf << "." << endl);
|
---|
1081 | // remove every bond from the list
|
---|
1082 | bond *Binder = NULL;
|
---|
1083 | while (Leaf->last->previous != Leaf->first) {
|
---|
1084 | Binder = Leaf->last->previous;
|
---|
1085 | Binder->leftatom->UnregisterBond(Binder);
|
---|
1086 | Binder->rightatom->UnregisterBond(Binder);
|
---|
1087 | removewithoutcheck(Binder);
|
---|
1088 | }
|
---|
1089 |
|
---|
1090 | Walker = Leaf->start;
|
---|
1091 | while (Walker->next != Leaf->end) {
|
---|
1092 | Walker = Walker->next;
|
---|
1093 | Father = Walker->GetTrueFather();
|
---|
1094 | AtomNo = Father->nr; // global id of the current walker
|
---|
1095 | for (BondList::const_iterator Runner = Father->ListOfBonds.begin(); Runner != Father->ListOfBonds.end(); (++Runner)) {
|
---|
1096 | OtherWalker = ListOfLocalAtoms[FragmentCounter][(*Runner)->GetOtherAtom(Walker->GetTrueFather())->nr]; // local copy of current bond partner of walker
|
---|
1097 | if (OtherWalker != NULL) {
|
---|
1098 | if (OtherWalker->nr > Walker->nr)
|
---|
1099 | Leaf->AddBond(Walker, OtherWalker, (*Runner)->BondDegree);
|
---|
1100 | } else {
|
---|
1101 | DoLog(1) && (Log() << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << FragmentCounter << "][" << (*Runner)->GetOtherAtom(Walker->GetTrueFather())->nr << "] is NULL!" << endl);
|
---|
1102 | status = false;
|
---|
1103 | }
|
---|
1104 | }
|
---|
1105 | }
|
---|
1106 | }
|
---|
1107 |
|
---|
1108 | if ((FreeList) && (ListOfLocalAtoms != NULL)) {
|
---|
1109 | // free the index lookup list
|
---|
1110 | Free(&ListOfLocalAtoms[FragmentCounter]);
|
---|
1111 | if (FragmentCounter == 0) // first fragments frees the initial pointer to list
|
---|
1112 | Free(&ListOfLocalAtoms);
|
---|
1113 | }
|
---|
1114 | DoLog(1) && (Log() << Verbose(1) << "End of FillBondStructureFromReference." << endl);
|
---|
1115 | return status;
|
---|
1116 | };
|
---|
1117 |
|
---|
1118 | /** Fills the root stack for sites to be used as root in fragmentation depending on order or adaptivity criteria
|
---|
1119 | * Again, as in \sa FillBondStructureFromReference steps recursively through each Leaf in this chain list of molecule's.
|
---|
1120 | * \param *out output stream for debugging
|
---|
1121 | * \param *&RootStack stack to be filled
|
---|
1122 | * \param *AtomMask defines true/false per global Atom::nr to mask in/out each nuclear site
|
---|
1123 | * \param &FragmentCounter counts through the fragments in this MoleculeLeafClass
|
---|
1124 | * \return true - stack is non-empty, fragmentation necessary, false - stack is empty, no more sites to update
|
---|
1125 | */
|
---|
1126 | bool MoleculeLeafClass::FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter)
|
---|
1127 | {
|
---|
1128 | atom *Walker = NULL, *Father = NULL;
|
---|
1129 |
|
---|
1130 | if (RootStack != NULL) {
|
---|
1131 | // find first root candidates
|
---|
1132 | if (&(RootStack[FragmentCounter]) != NULL) {
|
---|
1133 | RootStack[FragmentCounter].clear();
|
---|
1134 | Walker = Leaf->start;
|
---|
1135 | while (Walker->next != Leaf->end) { // go through all (non-hydrogen) atoms
|
---|
1136 | Walker = Walker->next;
|
---|
1137 | Father = Walker->GetTrueFather();
|
---|
1138 | if (AtomMask[Father->nr]) // apply mask
|
---|
1139 | #ifdef ADDHYDROGEN
|
---|
1140 | if (Walker->type->Z != 1) // skip hydrogen
|
---|
1141 | #endif
|
---|
1142 | RootStack[FragmentCounter].push_front(Walker->nr);
|
---|
1143 | }
|
---|
1144 | if (next != NULL)
|
---|
1145 | next->FillRootStackForSubgraphs(RootStack, AtomMask, ++FragmentCounter);
|
---|
1146 | } else {
|
---|
1147 | DoLog(1) && (Log() << Verbose(1) << "Rootstack[" << FragmentCounter << "] is NULL." << endl);
|
---|
1148 | return false;
|
---|
1149 | }
|
---|
1150 | FragmentCounter--;
|
---|
1151 | return true;
|
---|
1152 | } else {
|
---|
1153 | DoLog(1) && (Log() << Verbose(1) << "Rootstack is NULL." << endl);
|
---|
1154 | return false;
|
---|
1155 | }
|
---|
1156 | };
|
---|
1157 |
|
---|
1158 | /** Fills a lookup list of father's Atom::nr -> atom for each subgraph.
|
---|
1159 | * \param *out output stream from debugging
|
---|
1160 | * \param ***ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
|
---|
1161 | * \param FragmentCounter counts the fragments as we move along the list
|
---|
1162 | * \param GlobalAtomCount number of atoms in the complete molecule
|
---|
1163 | * \param &FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
|
---|
1164 | * \return true - success, false - failure
|
---|
1165 | */
|
---|
1166 | bool MoleculeLeafClass::FillListOfLocalAtoms(atom ***&ListOfLocalAtoms, const int FragmentCounter, const int GlobalAtomCount, bool &FreeList)
|
---|
1167 | {
|
---|
1168 | bool status = true;
|
---|
1169 |
|
---|
1170 | if (ListOfLocalAtoms == NULL) { // allocated initial pointer
|
---|
1171 | // allocate and set each field to NULL
|
---|
1172 | const int Counter = Count();
|
---|
1173 | ListOfLocalAtoms = Calloc<atom**>(Counter, "MoleculeLeafClass::FillListOfLocalAtoms - ***ListOfLocalAtoms");
|
---|
1174 | if (ListOfLocalAtoms == NULL) {
|
---|
1175 | FreeList = FreeList && false;
|
---|
1176 | status = false;
|
---|
1177 | }
|
---|
1178 | }
|
---|
1179 |
|
---|
1180 | if ((ListOfLocalAtoms != NULL) && (ListOfLocalAtoms[FragmentCounter] == NULL)) { // allocate and fill list of this fragment/subgraph
|
---|
1181 | status = status && CreateFatherLookupTable(Leaf->start, Leaf->end, ListOfLocalAtoms[FragmentCounter], GlobalAtomCount);
|
---|
1182 | FreeList = FreeList && true;
|
---|
1183 | }
|
---|
1184 |
|
---|
1185 | return status;
|
---|
1186 | };
|
---|
1187 |
|
---|
1188 | /** The indices per keyset are compared to the respective father's Atom::nr in each subgraph and thus put into \a **&FragmentList.
|
---|
1189 | * \param *out output stream fro debugging
|
---|
1190 | * \param *reference reference molecule with the bond structure to be copied
|
---|
1191 | * \param *KeySetList list with all keysets
|
---|
1192 | * \param ***ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
|
---|
1193 | * \param **&FragmentList list to be allocated and returned
|
---|
1194 | * \param &FragmentCounter counts the fragments as we move along the list
|
---|
1195 | * \param FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
|
---|
1196 | * \retuen true - success, false - failure
|
---|
1197 | */
|
---|
1198 | bool MoleculeLeafClass::AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList)
|
---|
1199 | {
|
---|
1200 | bool status = true;
|
---|
1201 | int KeySetCounter = 0;
|
---|
1202 |
|
---|
1203 | DoLog(1) && (Log() << Verbose(1) << "Begin of AssignKeySetsToFragment." << endl);
|
---|
1204 | // fill ListOfLocalAtoms if NULL was given
|
---|
1205 | if (!FillListOfLocalAtoms(ListOfLocalAtoms, FragmentCounter, reference->AtomCount, FreeList)) {
|
---|
1206 | DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
|
---|
1207 | return false;
|
---|
1208 | }
|
---|
1209 |
|
---|
1210 | // allocate fragment list
|
---|
1211 | if (FragmentList == NULL) {
|
---|
1212 | KeySetCounter = Count();
|
---|
1213 | FragmentList = Calloc<Graph*>(KeySetCounter, "MoleculeLeafClass::AssignKeySetsToFragment - **FragmentList");
|
---|
1214 | KeySetCounter = 0;
|
---|
1215 | }
|
---|
1216 |
|
---|
1217 | if ((KeySetList != NULL) && (KeySetList->size() != 0)) { // if there are some scanned keysets at all
|
---|
1218 | // assign scanned keysets
|
---|
1219 | if (FragmentList[FragmentCounter] == NULL)
|
---|
1220 | FragmentList[FragmentCounter] = new Graph;
|
---|
1221 | KeySet *TempSet = new KeySet;
|
---|
1222 | for (Graph::iterator runner = KeySetList->begin(); runner != KeySetList->end(); runner++) { // key sets contain global numbers!
|
---|
1223 | if (ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*((*runner).first.begin()))->nr] != NULL) {// as we may assume that that bond structure is unchanged, we only test the first key in each set
|
---|
1224 | // translate keyset to local numbers
|
---|
1225 | for (KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
|
---|
1226 | TempSet->insert(ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*sprinter)->nr]->nr);
|
---|
1227 | // insert into FragmentList
|
---|
1228 | FragmentList[FragmentCounter]->insert(GraphPair(*TempSet, pair<int, double> (KeySetCounter++, (*runner).second.second)));
|
---|
1229 | }
|
---|
1230 | TempSet->clear();
|
---|
1231 | }
|
---|
1232 | delete (TempSet);
|
---|
1233 | if (KeySetCounter == 0) {// if there are no keysets, delete the list
|
---|
1234 | DoLog(1) && (Log() << Verbose(1) << "KeySetCounter is zero, deleting FragmentList." << endl);
|
---|
1235 | delete (FragmentList[FragmentCounter]);
|
---|
1236 | } else
|
---|
1237 | DoLog(1) && (Log() << Verbose(1) << KeySetCounter << " keysets were assigned to subgraph " << FragmentCounter << "." << endl);
|
---|
1238 | FragmentCounter++;
|
---|
1239 | if (next != NULL)
|
---|
1240 | next->AssignKeySetsToFragment(reference, KeySetList, ListOfLocalAtoms, FragmentList, FragmentCounter, FreeList);
|
---|
1241 | FragmentCounter--;
|
---|
1242 | } else
|
---|
1243 | DoLog(1) && (Log() << Verbose(1) << "KeySetList is NULL or empty." << endl);
|
---|
1244 |
|
---|
1245 | if ((FreeList) && (ListOfLocalAtoms != NULL)) {
|
---|
1246 | // free the index lookup list
|
---|
1247 | Free(&ListOfLocalAtoms[FragmentCounter]);
|
---|
1248 | if (FragmentCounter == 0) // first fragments frees the initial pointer to list
|
---|
1249 | Free(&ListOfLocalAtoms);
|
---|
1250 | }
|
---|
1251 | DoLog(1) && (Log() << Verbose(1) << "End of AssignKeySetsToFragment." << endl);
|
---|
1252 | return status;
|
---|
1253 | };
|
---|
1254 |
|
---|
1255 | /** Translate list into global numbers (i.e. ones that are valid in "this" molecule, not in MolecularWalker->Leaf)
|
---|
1256 | * \param *out output stream for debugging
|
---|
1257 | * \param **FragmentList Graph with local numbers per fragment
|
---|
1258 | * \param &FragmentCounter counts the fragments as we move along the list
|
---|
1259 | * \param &TotalNumberOfKeySets global key set counter
|
---|
1260 | * \param &TotalGraph Graph to be filled with global numbers
|
---|
1261 | */
|
---|
1262 | void MoleculeLeafClass::TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph)
|
---|
1263 | {
|
---|
1264 | DoLog(1) && (Log() << Verbose(1) << "Begin of TranslateIndicesToGlobalIDs." << endl);
|
---|
1265 | KeySet *TempSet = new KeySet;
|
---|
1266 | if (FragmentList[FragmentCounter] != NULL) {
|
---|
1267 | for (Graph::iterator runner = FragmentList[FragmentCounter]->begin(); runner != FragmentList[FragmentCounter]->end(); runner++) {
|
---|
1268 | for (KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
|
---|
1269 | TempSet->insert((Leaf->FindAtom(*sprinter))->GetTrueFather()->nr);
|
---|
1270 | TotalGraph.insert(GraphPair(*TempSet, pair<int, double> (TotalNumberOfKeySets++, (*runner).second.second)));
|
---|
1271 | TempSet->clear();
|
---|
1272 | }
|
---|
1273 | delete (TempSet);
|
---|
1274 | } else {
|
---|
1275 | DoLog(1) && (Log() << Verbose(1) << "FragmentList is NULL." << endl);
|
---|
1276 | }
|
---|
1277 | if (next != NULL)
|
---|
1278 | next->TranslateIndicesToGlobalIDs(FragmentList, ++FragmentCounter, TotalNumberOfKeySets, TotalGraph);
|
---|
1279 | FragmentCounter--;
|
---|
1280 | DoLog(1) && (Log() << Verbose(1) << "End of TranslateIndicesToGlobalIDs." << endl);
|
---|
1281 | };
|
---|
1282 |
|
---|
1283 | /** Simply counts the number of items in the list, from given MoleculeLeafClass.
|
---|
1284 | * \return number of items
|
---|
1285 | */
|
---|
1286 | int MoleculeLeafClass::Count() const
|
---|
1287 | {
|
---|
1288 | if (next != NULL)
|
---|
1289 | return next->Count() + 1;
|
---|
1290 | else
|
---|
1291 | return 1;
|
---|
1292 | };
|
---|
1293 |
|
---|