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 University of Bonn. All rights reserved.
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5 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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6 | */
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7 |
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8 | /** \file MoleculeListClass.cpp
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9 | *
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10 | * Function implementations for the class MoleculeListClass.
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11 | *
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12 | */
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13 |
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14 | // include config.h
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15 | #ifdef HAVE_CONFIG_H
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16 | #include <config.h>
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17 | #endif
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18 |
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19 | #include "CodePatterns/MemDebug.hpp"
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20 |
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21 | #include <cstring>
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22 |
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23 | #include <gsl/gsl_inline.h>
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24 | #include <gsl/gsl_heapsort.h>
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25 |
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26 | #include "atom.hpp"
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27 | #include "Bond/bond.hpp"
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28 | #include "boundary.hpp"
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29 | #include "Box.hpp"
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30 | #include "CodePatterns/Assert.hpp"
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31 | #include "CodePatterns/Log.hpp"
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32 | #include "CodePatterns/Verbose.hpp"
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33 | #include "config.hpp"
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34 | #include "element.hpp"
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35 | #include "Graph/BondGraph.hpp"
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36 | #include "Helpers/fast_functions.hpp"
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37 | #include "Helpers/helpers.hpp"
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38 | #include "LinearAlgebra/RealSpaceMatrix.hpp"
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39 | #include "linkedcell.hpp"
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40 | #include "molecule.hpp"
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41 | #include "periodentafel.hpp"
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42 | #include "tesselation.hpp"
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43 | #include "World.hpp"
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44 | #include "WorldTime.hpp"
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45 |
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46 | /*********************************** Functions for class MoleculeListClass *************************/
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47 |
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48 | /** Constructor for MoleculeListClass.
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49 | */
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50 | MoleculeListClass::MoleculeListClass(World *_world) :
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51 | Observable("MoleculeListClass"),
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52 | MaxIndex(1),
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53 | world(_world)
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54 | {};
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55 |
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56 | /** Destructor for MoleculeListClass.
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57 | */
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58 | MoleculeListClass::~MoleculeListClass()
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59 | {
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60 | DoLog(4) && (Log() << Verbose(4) << "Clearing ListOfMolecules." << endl);
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61 | for(MoleculeList::iterator MolRunner = ListOfMolecules.begin(); MolRunner != ListOfMolecules.end(); ++MolRunner)
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62 | (*MolRunner)->signOff(this);
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63 | ListOfMolecules.clear(); // empty list
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64 | };
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65 |
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66 | /** Insert a new molecule into the list and set its number.
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67 | * \param *mol molecule to add to list.
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68 | */
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69 | void MoleculeListClass::insert(molecule *mol)
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70 | {
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71 | OBSERVE;
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72 | mol->IndexNr = MaxIndex++;
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73 | ListOfMolecules.push_back(mol);
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74 | mol->signOn(this);
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75 | };
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76 |
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77 | /** Erases a molecule from the list.
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78 | * \param *mol molecule to add to list.
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79 | */
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80 | void MoleculeListClass::erase(molecule *mol)
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81 | {
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82 | OBSERVE;
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83 | mol->signOff(this);
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84 | ListOfMolecules.remove(mol);
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85 | };
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86 |
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87 | /** Comparison function for two values.
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88 | * \param *a
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89 | * \param *b
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90 | * \return <0, \a *a less than \a *b, ==0 if equal, >0 \a *a greater than \a *b
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91 | */
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92 | int CompareDoubles (const void * a, const void * b)
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93 | {
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94 | if (*(double *)a > *(double *)b)
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95 | return -1;
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96 | else if (*(double *)a < *(double *)b)
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97 | return 1;
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98 | else
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99 | return 0;
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100 | };
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101 |
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102 |
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103 | /** Compare whether two molecules are equal.
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104 | * \param *a molecule one
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105 | * \param *n molecule two
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106 | * \return lexical value (-1, 0, +1)
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107 | */
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108 | int MolCompare(const void *a, const void *b)
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109 | {
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110 | int *aList = NULL, *bList = NULL;
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111 | int Count, Counter, aCounter, bCounter;
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112 | int flag;
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113 |
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114 | // sort each atom list and put the numbers into a list, then go through
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115 | //Log() << Verbose(0) << "Comparing fragment no. " << *(molecule **)a << " to " << *(molecule **)b << "." << endl;
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116 | // Yes those types are awkward... but check it for yourself it checks out this way
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117 | molecule *const *mol1_ptr= static_cast<molecule *const *>(a);
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118 | molecule *mol1 = *mol1_ptr;
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119 | molecule *const *mol2_ptr= static_cast<molecule *const *>(b);
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120 | molecule *mol2 = *mol2_ptr;
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121 | if (mol1->getAtomCount() < mol2->getAtomCount()) {
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122 | return -1;
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123 | } else {
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124 | if (mol1->getAtomCount() > mol2->getAtomCount())
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125 | return +1;
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126 | else {
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127 | Count = mol1->getAtomCount();
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128 | aList = new int[Count];
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129 | bList = new int[Count];
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130 |
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131 | // fill the lists
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132 | Counter = 0;
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133 | aCounter = 0;
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134 | bCounter = 0;
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135 | molecule::const_iterator aiter = mol1->begin();
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136 | molecule::const_iterator biter = mol2->begin();
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137 | for (;(aiter != mol1->end()) && (biter != mol2->end());
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138 | ++aiter, ++biter) {
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139 | if ((*aiter)->GetTrueFather() == NULL)
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140 | aList[Counter] = Count + (aCounter++);
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141 | else
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142 | aList[Counter] = (*aiter)->GetTrueFather()->getNr();
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143 | if ((*biter)->GetTrueFather() == NULL)
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144 | bList[Counter] = Count + (bCounter++);
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145 | else
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146 | bList[Counter] = (*biter)->GetTrueFather()->getNr();
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147 | Counter++;
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148 | }
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149 | // check if AtomCount was for real
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150 | flag = 0;
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151 | if ((aiter == mol1->end()) && (biter != mol2->end())) {
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152 | flag = -1;
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153 | } else {
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154 | if ((aiter != mol1->end()) && (biter == mol2->end()))
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155 | flag = 1;
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156 | }
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157 | if (flag == 0) {
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158 | // sort the lists
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159 | gsl_heapsort(aList, Count, sizeof(int), CompareDoubles);
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160 | gsl_heapsort(bList, Count, sizeof(int), CompareDoubles);
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161 | // compare the lists
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162 |
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163 | flag = 0;
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164 | for (int i = 0; i < Count; i++) {
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165 | if (aList[i] < bList[i]) {
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166 | flag = -1;
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167 | } else {
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168 | if (aList[i] > bList[i])
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169 | flag = 1;
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170 | }
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171 | if (flag != 0)
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172 | break;
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173 | }
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174 | }
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175 | delete[] (aList);
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176 | delete[] (bList);
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177 | return flag;
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178 | }
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179 | }
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180 | return -1;
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181 | };
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182 |
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183 | /** Output of a list of all molecules.
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184 | * \param *out output stream
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185 | */
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186 | void MoleculeListClass::Enumerate(ostream *out)
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187 | {
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188 | periodentafel *periode = World::getInstance().getPeriode();
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189 | std::map<atomicNumber_t,unsigned int> counts;
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190 | double size=0;
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191 | Vector Origin;
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192 |
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193 | // header
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194 | (*out) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
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195 | (*out) << "-----------------------------------------------" << endl;
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196 | if (ListOfMolecules.size() == 0)
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197 | (*out) << "\tNone" << endl;
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198 | else {
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199 | Origin.Zero();
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200 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
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201 | // count atoms per element and determine size of bounding sphere
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202 | size=0.;
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203 | for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
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204 | counts[(*iter)->getType()->getNumber()]++;
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205 | if ((*iter)->DistanceSquared(Origin) > size)
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206 | size = (*iter)->DistanceSquared(Origin);
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207 | }
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208 | // output Index, Name, number of atoms, chemical formula
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209 | (*out) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->getAtomCount() << "\t";
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210 |
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211 | std::map<atomicNumber_t,unsigned int>::reverse_iterator iter;
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212 | for(iter=counts.rbegin(); iter!=counts.rend();++iter){
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213 | atomicNumber_t Z =(*iter).first;
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214 | (*out) << periode->FindElement(Z)->getSymbol() << (*iter).second;
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215 | }
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216 | // Center and size
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217 | Vector *Center = (*ListRunner)->DetermineCenterOfAll();
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218 | (*out) << "\t" << *Center << "\t" << sqrt(size) << endl;
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219 | delete(Center);
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220 | }
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221 | }
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222 | };
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223 |
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224 | /** Returns the molecule with the given index \a index.
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225 | * \param index index of the desired molecule
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226 | * \return pointer to molecule structure, NULL if not found
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227 | */
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228 | molecule * MoleculeListClass::ReturnIndex(int index)
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229 | {
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230 | for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
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231 | if ((*ListRunner)->IndexNr == index)
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232 | return (*ListRunner);
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233 | return NULL;
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234 | };
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235 |
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236 |
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237 | /** Simple output of the pointers in ListOfMolecules.
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238 | * \param *out output stream
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239 | */
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240 | void MoleculeListClass::Output(ofstream *out)
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241 | {
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242 | DoLog(1) && (Log() << Verbose(1) << "MoleculeList: ");
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243 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
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244 | DoLog(0) && (Log() << Verbose(0) << *ListRunner << "\t");
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245 | DoLog(0) && (Log() << Verbose(0) << endl);
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246 | };
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247 |
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248 | /** Calculates necessary hydrogen correction due to unwanted interaction between saturated ones.
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249 | * 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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250 | * bonded to the same atom, then we add for this pair a correction term constructed from a Morse
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251 | * potential function fit to QM calculations with respecting to the interatomic hydrogen distance.
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252 | * \param &path path to file
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253 | */
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254 | bool MoleculeListClass::AddHydrogenCorrection(std::string &path)
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255 | {
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256 | bond *Binder = NULL;
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257 | double ***FitConstant = NULL, **correction = NULL;
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258 | int a, b;
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259 | ofstream output;
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260 | ifstream input;
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261 | string line;
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262 | stringstream zeile;
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263 | double distance;
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264 | char ParsedLine[1023];
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265 | double tmp;
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266 | char *FragmentNumber = NULL;
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267 |
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268 | DoLog(1) && (Log() << Verbose(1) << "Saving hydrogen saturation correction ... ");
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269 | // 0. parse in fit constant files that should have the same dimension as the final energy files
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270 | // 0a. find dimension of matrices with constants
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271 | line = path;
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272 | line += "1";
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273 | line += FITCONSTANTSUFFIX;
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274 | input.open(line.c_str());
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275 | if (input.fail()) {
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276 | DoLog(1) && (Log() << Verbose(1) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
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277 | return false;
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278 | }
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279 | a = 0;
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280 | b = -1; // we overcount by one
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281 | while (!input.eof()) {
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282 | input.getline(ParsedLine, 1023);
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283 | zeile.str(ParsedLine);
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284 | int i = 0;
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285 | while (!zeile.eof()) {
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286 | zeile >> distance;
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287 | i++;
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288 | }
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289 | if (i > a)
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290 | a = i;
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291 | b++;
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292 | }
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293 | DoLog(0) && (Log() << Verbose(0) << "I recognized " << a << " columns and " << b << " rows, ");
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294 | input.close();
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295 |
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296 | // 0b. allocate memory for constants
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297 | FitConstant = new double**[3];
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298 | for (int k = 0; k < 3; k++) {
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299 | FitConstant[k] = new double*[a];
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300 | for (int i = a; i--;) {
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301 | FitConstant[k][i] = new double[b];
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302 | for (int j = b; j--;) {
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303 | FitConstant[k][i][j] = 0.;
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304 | }
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305 | }
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306 | }
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307 | // 0c. parse in constants
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308 | for (int i = 0; i < 3; i++) {
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309 | line = path;
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310 | line.append("/");
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311 | line += FRAGMENTPREFIX;
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312 | sprintf(ParsedLine, "%d", i + 1);
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313 | line += ParsedLine;
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314 | line += FITCONSTANTSUFFIX;
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315 | input.open(line.c_str());
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316 | if (input == NULL) {
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317 | DoeLog(0) && (eLog()<< Verbose(0) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
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318 | performCriticalExit();
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319 | return false;
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320 | }
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321 | int k = 0, l;
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322 | while ((!input.eof()) && (k < b)) {
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323 | input.getline(ParsedLine, 1023);
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324 | //Log() << Verbose(0) << "Current Line: " << ParsedLine << endl;
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325 | zeile.str(ParsedLine);
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326 | zeile.clear();
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327 | l = 0;
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328 | while ((!zeile.eof()) && (l < a)) {
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329 | zeile >> FitConstant[i][l][k];
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330 | //Log() << Verbose(0) << FitConstant[i][l][k] << "\t";
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331 | l++;
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332 | }
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333 | //Log() << Verbose(0) << endl;
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334 | k++;
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335 | }
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336 | input.close();
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337 | }
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338 | for (int k = 0; k < 3; k++) {
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339 | DoLog(0) && (Log() << Verbose(0) << "Constants " << k << ":" << endl);
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340 | for (int j = 0; j < b; j++) {
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341 | for (int i = 0; i < a; i++) {
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342 | DoLog(0) && (Log() << Verbose(0) << FitConstant[k][i][j] << "\t");
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343 | }
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344 | DoLog(0) && (Log() << Verbose(0) << endl);
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345 | }
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346 | DoLog(0) && (Log() << Verbose(0) << endl);
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347 | }
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348 |
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349 | // 0d. allocate final correction matrix
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350 | correction = new double*[a];
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351 | for (int i = a; i--;)
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352 | correction[i] = new double[b];
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353 |
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354 | // 1a. go through every molecule in the list
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355 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
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356 | // 1b. zero final correction matrix
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357 | for (int k = a; k--;)
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358 | for (int j = b; j--;)
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359 | correction[k][j] = 0.;
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360 | // 2. take every hydrogen that is a saturated one
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361 | for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
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362 | //Log() << Verbose(1) << "(*iter): " << *(*iter) << " with first bond " << *((*iter)->getListOfBonds().begin()) << "." << endl;
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363 | if (((*iter)->getType()->getAtomicNumber() == 1) && (((*iter)->father == NULL)
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364 | || ((*iter)->father->getType()->getAtomicNumber() != 1))) { // if it's a hydrogen
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365 | for (molecule::const_iterator runner = (*ListRunner)->begin(); runner != (*ListRunner)->end(); ++runner) {
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366 | //Log() << Verbose(2) << "Runner: " << *(*runner) << " with first bond " << *((*iter)->getListOfBonds().begin()) << "." << endl;
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367 | // 3. take every other hydrogen that is the not the first and not bound to same bonding partner
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368 | Binder = *((*runner)->getListOfBonds().begin());
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369 | if (((*runner)->getType()->getAtomicNumber() == 1) && ((*runner)->getNr() > (*iter)->getNr()) && (Binder->GetOtherAtom((*runner)) != Binder->GetOtherAtom((*iter)))) { // (hydrogens have only one bonding partner!)
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370 | // 4. evaluate the morse potential for each matrix component and add up
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371 | distance = (*runner)->distance(*(*iter));
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372 | //Log() << Verbose(0) << "Fragment " << (*ListRunner)->name << ": " << *(*runner) << "<= " << distance << "=>" << *(*iter) << ":" << endl;
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373 | for (int k = 0; k < a; k++) {
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374 | for (int j = 0; j < b; j++) {
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375 | switch (k) {
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376 | case 1:
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377 | case 7:
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378 | case 11:
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379 | tmp = pow(FitConstant[0][k][j] * (1. - exp(-FitConstant[1][k][j] * (distance - FitConstant[2][k][j]))), 2);
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380 | break;
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381 | default:
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382 | tmp = FitConstant[0][k][j] * pow(distance, FitConstant[1][k][j]) + FitConstant[2][k][j];
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383 | };
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384 | correction[k][j] -= tmp; // ground state is actually lower (disturbed by additional interaction)
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385 | //Log() << Verbose(0) << tmp << "\t";
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386 | }
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387 | //Log() << Verbose(0) << endl;
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388 | }
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389 | //Log() << Verbose(0) << endl;
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390 | }
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391 | }
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392 | }
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393 | }
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394 | // 5. write final matrix to file
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395 | line = path;
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396 | line.append("/");
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397 | line += FRAGMENTPREFIX;
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398 | FragmentNumber = FixedDigitNumber(ListOfMolecules.size(), (*ListRunner)->IndexNr);
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399 | line += FragmentNumber;
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400 | delete[] (FragmentNumber);
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401 | line += HCORRECTIONSUFFIX;
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402 | output.open(line.c_str());
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403 | output << "Time\t\tTotal\t\tKinetic\t\tNonLocal\tCorrelation\tExchange\tPseudo\t\tHartree\t\t-Gauss\t\tEwald\t\tIonKin\t\tETotal" << endl;
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404 | for (int j = 0; j < b; j++) {
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405 | for (int i = 0; i < a; i++)
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406 | output << correction[i][j] << "\t";
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407 | output << endl;
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408 | }
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409 | output.close();
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410 | }
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411 | for (int i = a; i--;)
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412 | delete[](correction[i]);
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413 | delete[](correction);
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414 |
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415 | line = path;
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416 | line.append("/");
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417 | line += HCORRECTIONSUFFIX;
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418 | output.open(line.c_str());
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419 | output << "Time\t\tTotal\t\tKinetic\t\tNonLocal\tCorrelation\tExchange\tPseudo\t\tHartree\t\t-Gauss\t\tEwald\t\tIonKin\t\tETotal" << endl;
|
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420 | for (int j = 0; j < b; j++) {
|
---|
421 | for (int i = 0; i < a; i++)
|
---|
422 | output << 0 << "\t";
|
---|
423 | output << endl;
|
---|
424 | }
|
---|
425 | output.close();
|
---|
426 | // 6. free memory of parsed matrices
|
---|
427 | for (int k = 0; k < 3; k++) {
|
---|
428 | for (int i = a; i--;) {
|
---|
429 | delete[](FitConstant[k][i]);
|
---|
430 | }
|
---|
431 | delete[](FitConstant[k]);
|
---|
432 | }
|
---|
433 | delete[](FitConstant);
|
---|
434 | DoLog(0) && (Log() << Verbose(0) << "done." << endl);
|
---|
435 | return true;
|
---|
436 | };
|
---|
437 |
|
---|
438 | /** Store force indices, i.e. the connection between the nuclear index in the total molecule config and the respective atom in fragment config.
|
---|
439 | * \param &path path to file
|
---|
440 | * \param *SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
|
---|
441 | * \return true - file written successfully, false - writing failed
|
---|
442 | */
|
---|
443 | bool MoleculeListClass::StoreForcesFile(std::string &path, int *SortIndex)
|
---|
444 | {
|
---|
445 | bool status = true;
|
---|
446 | string filename(path);
|
---|
447 | filename += FORCESFILE;
|
---|
448 | ofstream ForcesFile(filename.c_str());
|
---|
449 | periodentafel *periode=World::getInstance().getPeriode();
|
---|
450 |
|
---|
451 | // open file for the force factors
|
---|
452 | DoLog(1) && (Log() << Verbose(1) << "Saving force factors ... ");
|
---|
453 | if (!ForcesFile.fail()) {
|
---|
454 | //Log() << Verbose(1) << "Final AtomicForcesList: ";
|
---|
455 | //output << prefix << "Forces" << endl;
|
---|
456 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
|
---|
457 | periodentafel::const_iterator elemIter;
|
---|
458 | for(elemIter=periode->begin();elemIter!=periode->end();++elemIter){
|
---|
459 | if ((*ListRunner)->hasElement((*elemIter).first)) { // if this element got atoms
|
---|
460 | for(molecule::iterator atomIter = (*ListRunner)->begin(); atomIter !=(*ListRunner)->end();++atomIter){
|
---|
461 | if ((*atomIter)->getType()->getNumber() == (*elemIter).first) {
|
---|
462 | if (((*atomIter)->GetTrueFather() != NULL) && ((*atomIter)->GetTrueFather() != (*atomIter))) {// if there is a rea
|
---|
463 | //Log() << Verbose(0) << "Walker is " << *Walker << " with true father " << *( Walker->GetTrueFather()) << ", it
|
---|
464 | ForcesFile << SortIndex[(*atomIter)->GetTrueFather()->getNr()] << "\t";
|
---|
465 | } else
|
---|
466 | // otherwise a -1 to indicate an added saturation hydrogen
|
---|
467 | ForcesFile << "-1\t";
|
---|
468 | }
|
---|
469 | }
|
---|
470 | }
|
---|
471 | }
|
---|
472 | ForcesFile << endl;
|
---|
473 | }
|
---|
474 | ForcesFile.close();
|
---|
475 | DoLog(1) && (Log() << Verbose(1) << "done." << endl);
|
---|
476 | } else {
|
---|
477 | status = false;
|
---|
478 | DoLog(1) && (Log() << Verbose(1) << "failed to open file " << filename << "." << endl);
|
---|
479 | }
|
---|
480 | ForcesFile.close();
|
---|
481 |
|
---|
482 | return status;
|
---|
483 | };
|
---|
484 |
|
---|
485 | /** Writes a config file for each molecule in the given \a **FragmentList.
|
---|
486 | * \param *out output stream for debugging
|
---|
487 | * \param &prefix path and prefix to the fragment config files
|
---|
488 | * \param *SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
|
---|
489 | * \return true - success (each file was written), false - something went wrong.
|
---|
490 | */
|
---|
491 | bool MoleculeListClass::OutputConfigForListOfFragments(std::string &prefix, int *SortIndex)
|
---|
492 | {
|
---|
493 | ofstream outputFragment;
|
---|
494 | std::string FragmentName;
|
---|
495 | char PathBackup[MAXSTRINGSIZE];
|
---|
496 | bool result = true;
|
---|
497 | bool intermediateResult = true;
|
---|
498 | Vector BoxDimension;
|
---|
499 | char *FragmentNumber = NULL;
|
---|
500 | char *path = NULL;
|
---|
501 | int FragmentCounter = 0;
|
---|
502 | ofstream output;
|
---|
503 | RealSpaceMatrix cell_size = World::getInstance().getDomain().getM();
|
---|
504 | RealSpaceMatrix cell_size_backup = cell_size;
|
---|
505 | int count=0;
|
---|
506 |
|
---|
507 | // store the fragments as config and as xyz
|
---|
508 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
|
---|
509 | // save default path as it is changed for each fragment
|
---|
510 | path = World::getInstance().getConfig()->GetDefaultPath();
|
---|
511 | if (path != NULL)
|
---|
512 | strcpy(PathBackup, path);
|
---|
513 | else {
|
---|
514 | DoeLog(0) && (eLog()<< Verbose(0) << "OutputConfigForListOfFragments: NULL default path obtained from config!" << endl);
|
---|
515 | performCriticalExit();
|
---|
516 | }
|
---|
517 |
|
---|
518 | // correct periodic
|
---|
519 | if ((*ListRunner)->ScanForPeriodicCorrection()) {
|
---|
520 | count++;
|
---|
521 | }
|
---|
522 |
|
---|
523 | // output xyz file
|
---|
524 | FragmentNumber = FixedDigitNumber(ListOfMolecules.size(), FragmentCounter++);
|
---|
525 | FragmentName = prefix + FragmentNumber + ".conf.xyz";
|
---|
526 | outputFragment.open(FragmentName.c_str(), ios::out);
|
---|
527 | DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ...");
|
---|
528 | if ((intermediateResult = (*ListRunner)->OutputXYZ(&outputFragment)))
|
---|
529 | DoLog(0) && (Log() << Verbose(0) << " done." << endl);
|
---|
530 | else
|
---|
531 | DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
|
---|
532 | result = result && intermediateResult;
|
---|
533 | outputFragment.close();
|
---|
534 | outputFragment.clear();
|
---|
535 |
|
---|
536 | // list atoms in fragment for debugging
|
---|
537 | DoLog(2) && (Log() << Verbose(2) << "Contained atoms: ");
|
---|
538 | for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
|
---|
539 | DoLog(0) && (Log() << Verbose(0) << (*iter)->getName() << " ");
|
---|
540 | }
|
---|
541 | DoLog(0) && (Log() << Verbose(0) << endl);
|
---|
542 |
|
---|
543 | // center on edge
|
---|
544 | (*ListRunner)->CenterEdge(&BoxDimension);
|
---|
545 | for (int k = 0; k < NDIM; k++) // if one edge is to small, set at least to 1 angstroem
|
---|
546 | if (BoxDimension[k] < 1.)
|
---|
547 | BoxDimension[k] += 1.;
|
---|
548 | (*ListRunner)->SetBoxDimension(&BoxDimension); // update Box of atoms by boundary
|
---|
549 | for (int k = 0; k < NDIM; k++) {
|
---|
550 | BoxDimension[k] = 2.5 * (World::getInstance().getConfig()->GetIsAngstroem() ? 1. : 1. / AtomicLengthToAngstroem);
|
---|
551 | cell_size.at(k,k) = BoxDimension[k] * 2.;
|
---|
552 | }
|
---|
553 | World::getInstance().setDomain(cell_size);
|
---|
554 | (*ListRunner)->Translate(&BoxDimension);
|
---|
555 |
|
---|
556 | // also calculate necessary orbitals
|
---|
557 | //(*ListRunner)->CalculateOrbitals(*World::getInstance().getConfig);
|
---|
558 |
|
---|
559 | // change path in config
|
---|
560 | FragmentName = PathBackup;
|
---|
561 | FragmentName += "/";
|
---|
562 | FragmentName += FRAGMENTPREFIX;
|
---|
563 | FragmentName += FragmentNumber;
|
---|
564 | FragmentName += "/";
|
---|
565 | World::getInstance().getConfig()->SetDefaultPath(FragmentName.c_str());
|
---|
566 |
|
---|
567 | // and save as config
|
---|
568 | FragmentName = prefix + FragmentNumber + ".conf";
|
---|
569 | DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as config ...");
|
---|
570 | if ((intermediateResult = World::getInstance().getConfig()->Save(FragmentName.c_str(), (*ListRunner)->elemente, (*ListRunner))))
|
---|
571 | DoLog(0) && (Log() << Verbose(0) << " done." << endl);
|
---|
572 | else
|
---|
573 | DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
|
---|
574 | result = result && intermediateResult;
|
---|
575 |
|
---|
576 | // restore old config
|
---|
577 | World::getInstance().getConfig()->SetDefaultPath(PathBackup);
|
---|
578 |
|
---|
579 | // and save as mpqc input file
|
---|
580 | FragmentName = prefix + FragmentNumber + ".conf";
|
---|
581 | DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ...");
|
---|
582 | if ((intermediateResult = World::getInstance().getConfig()->SaveMPQC(FragmentName.c_str(), (*ListRunner))))
|
---|
583 | DoLog(2) && (Log() << Verbose(2) << " done." << endl);
|
---|
584 | else
|
---|
585 | DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
|
---|
586 |
|
---|
587 | result = result && intermediateResult;
|
---|
588 | //outputFragment.close();
|
---|
589 | //outputFragment.clear();
|
---|
590 | delete[](FragmentNumber);
|
---|
591 | }
|
---|
592 | DoLog(0) && (Log() << Verbose(0) << " done." << endl);
|
---|
593 |
|
---|
594 | // printing final number
|
---|
595 | DoLog(2) && (Log() << Verbose(2) << "Final number of fragments: " << FragmentCounter << "." << endl);
|
---|
596 |
|
---|
597 | // printing final number
|
---|
598 | DoLog(0) && (Log() << Verbose(0) << "For " << count << " fragments periodic correction would have been necessary." << endl);
|
---|
599 |
|
---|
600 | // restore cell_size
|
---|
601 | World::getInstance().setDomain(cell_size_backup);
|
---|
602 |
|
---|
603 | return result;
|
---|
604 | };
|
---|
605 |
|
---|
606 | /** Counts the number of molecules with the molecule::ActiveFlag set.
|
---|
607 | * \return number of molecules with ActiveFlag set to true.
|
---|
608 | */
|
---|
609 | int MoleculeListClass::NumberOfActiveMolecules()
|
---|
610 | {
|
---|
611 | int count = 0;
|
---|
612 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
|
---|
613 | count += ((*ListRunner)->ActiveFlag ? 1 : 0);
|
---|
614 | return count;
|
---|
615 | };
|
---|
616 |
|
---|
617 | /** Count all atoms in each molecule.
|
---|
618 | * \return number of atoms in the MoleculeListClass.
|
---|
619 | * TODO: the inner loop should be done by some (double molecule::CountAtom()) function
|
---|
620 | */
|
---|
621 | int MoleculeListClass::CountAllAtoms() const
|
---|
622 | {
|
---|
623 | int AtomNo = 0;
|
---|
624 | for (MoleculeList::const_iterator MolWalker = ListOfMolecules.begin(); MolWalker != ListOfMolecules.end(); MolWalker++) {
|
---|
625 | AtomNo += (*MolWalker)->size();
|
---|
626 | }
|
---|
627 | return AtomNo;
|
---|
628 | }
|
---|
629 |
|
---|
630 | /***********
|
---|
631 | * Methods Moved here from the menus
|
---|
632 | */
|
---|
633 |
|
---|
634 | void MoleculeListClass::createNewMolecule(periodentafel *periode) {
|
---|
635 | OBSERVE;
|
---|
636 | molecule *mol = NULL;
|
---|
637 | mol = World::getInstance().createMolecule();
|
---|
638 | insert(mol);
|
---|
639 | };
|
---|
640 |
|
---|
641 | void MoleculeListClass::loadFromXYZ(periodentafel *periode){
|
---|
642 | molecule *mol = NULL;
|
---|
643 | Vector center;
|
---|
644 | char filename[MAXSTRINGSIZE];
|
---|
645 | Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
|
---|
646 | mol = World::getInstance().createMolecule();
|
---|
647 | do {
|
---|
648 | Log() << Verbose(0) << "Enter file name: ";
|
---|
649 | cin >> filename;
|
---|
650 | } while (!mol->AddXYZFile(filename));
|
---|
651 | mol->SetNameFromFilename(filename);
|
---|
652 | // center at set box dimensions
|
---|
653 | mol->CenterEdge(¢er);
|
---|
654 | RealSpaceMatrix domain;
|
---|
655 | for(int i =0;i<NDIM;++i)
|
---|
656 | domain.at(i,i) = center[i];
|
---|
657 | World::getInstance().setDomain(domain);
|
---|
658 | insert(mol);
|
---|
659 | }
|
---|
660 |
|
---|
661 | void MoleculeListClass::setMoleculeFilename() {
|
---|
662 | char filename[MAXSTRINGSIZE];
|
---|
663 | int nr;
|
---|
664 | molecule *mol = NULL;
|
---|
665 | do {
|
---|
666 | Log() << Verbose(0) << "Enter index of molecule: ";
|
---|
667 | cin >> nr;
|
---|
668 | mol = ReturnIndex(nr);
|
---|
669 | } while (mol == NULL);
|
---|
670 | Log() << Verbose(0) << "Enter name: ";
|
---|
671 | cin >> filename;
|
---|
672 | mol->SetNameFromFilename(filename);
|
---|
673 | }
|
---|
674 |
|
---|
675 | void MoleculeListClass::parseXYZIntoMolecule(){
|
---|
676 | char filename[MAXSTRINGSIZE];
|
---|
677 | int nr;
|
---|
678 | molecule *mol = NULL;
|
---|
679 | mol = NULL;
|
---|
680 | do {
|
---|
681 | Log() << Verbose(0) << "Enter index of molecule: ";
|
---|
682 | cin >> nr;
|
---|
683 | mol = ReturnIndex(nr);
|
---|
684 | } while (mol == NULL);
|
---|
685 | Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
|
---|
686 | do {
|
---|
687 | Log() << Verbose(0) << "Enter file name: ";
|
---|
688 | cin >> filename;
|
---|
689 | } while (!mol->AddXYZFile(filename));
|
---|
690 | mol->SetNameFromFilename(filename);
|
---|
691 | };
|
---|
692 |
|
---|
693 | void MoleculeListClass::eraseMolecule(){
|
---|
694 | int nr;
|
---|
695 | molecule *mol = NULL;
|
---|
696 | Log() << Verbose(0) << "Enter index of molecule: ";
|
---|
697 | cin >> nr;
|
---|
698 | for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
|
---|
699 | if (nr == (*ListRunner)->IndexNr) {
|
---|
700 | mol = *ListRunner;
|
---|
701 | ListOfMolecules.erase(ListRunner);
|
---|
702 | World::getInstance().destroyMolecule(mol);
|
---|
703 | break;
|
---|
704 | }
|
---|
705 | };
|
---|
706 |
|
---|
707 |
|
---|
708 | /******************************************* Class MoleculeLeafClass ************************************************/
|
---|
709 |
|
---|
710 | /** Constructor for MoleculeLeafClass root leaf.
|
---|
711 | * \param *Up Leaf on upper level
|
---|
712 | * \param *PreviousLeaf NULL - We are the first leaf on this level, otherwise points to previous in list
|
---|
713 | */
|
---|
714 | //MoleculeLeafClass::MoleculeLeafClass(MoleculeLeafClass *Up = NULL, MoleculeLeafClass *Previous = NULL)
|
---|
715 | MoleculeLeafClass::MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf = NULL) :
|
---|
716 | Leaf(NULL),
|
---|
717 | previous(PreviousLeaf)
|
---|
718 | {
|
---|
719 | // if (Up != NULL)
|
---|
720 | // if (Up->DownLeaf == NULL) // are we the first down leaf for the upper leaf?
|
---|
721 | // Up->DownLeaf = this;
|
---|
722 | // UpLeaf = Up;
|
---|
723 | // DownLeaf = NULL;
|
---|
724 | if (previous != NULL) {
|
---|
725 | MoleculeLeafClass *Walker = previous->next;
|
---|
726 | previous->next = this;
|
---|
727 | next = Walker;
|
---|
728 | } else {
|
---|
729 | next = NULL;
|
---|
730 | }
|
---|
731 | };
|
---|
732 |
|
---|
733 | /** Destructor for MoleculeLeafClass.
|
---|
734 | */
|
---|
735 | MoleculeLeafClass::~MoleculeLeafClass()
|
---|
736 | {
|
---|
737 | // if (DownLeaf != NULL) {// drop leaves further down
|
---|
738 | // MoleculeLeafClass *Walker = DownLeaf;
|
---|
739 | // MoleculeLeafClass *Next;
|
---|
740 | // do {
|
---|
741 | // Next = Walker->NextLeaf;
|
---|
742 | // delete(Walker);
|
---|
743 | // Walker = Next;
|
---|
744 | // } while (Walker != NULL);
|
---|
745 | // // Last Walker sets DownLeaf automatically to NULL
|
---|
746 | // }
|
---|
747 | // remove the leaf itself
|
---|
748 | if (Leaf != NULL) {
|
---|
749 | Leaf->removeAtomsinMolecule();
|
---|
750 | World::getInstance().destroyMolecule(Leaf);
|
---|
751 | Leaf = NULL;
|
---|
752 | }
|
---|
753 | // remove this Leaf from level list
|
---|
754 | if (previous != NULL)
|
---|
755 | previous->next = next;
|
---|
756 | // } else { // we are first in list (connects to UpLeaf->DownLeaf)
|
---|
757 | // if ((NextLeaf != NULL) && (NextLeaf->UpLeaf == NULL))
|
---|
758 | // NextLeaf->UpLeaf = UpLeaf; // either null as we are top level or the upleaf of the first node
|
---|
759 | // if (UpLeaf != NULL)
|
---|
760 | // UpLeaf->DownLeaf = NextLeaf; // either null as we are only leaf or NextLeaf if we are just the first
|
---|
761 | // }
|
---|
762 | // UpLeaf = NULL;
|
---|
763 | if (next != NULL) // are we last in list
|
---|
764 | next->previous = previous;
|
---|
765 | next = NULL;
|
---|
766 | previous = NULL;
|
---|
767 | };
|
---|
768 |
|
---|
769 | /** Adds \a molecule leaf to the tree.
|
---|
770 | * \param *ptr ptr to molecule to be added
|
---|
771 | * \param *Previous previous MoleculeLeafClass referencing level and which on the level
|
---|
772 | * \return true - success, false - something went wrong
|
---|
773 | */
|
---|
774 | bool MoleculeLeafClass::AddLeaf(molecule *ptr, MoleculeLeafClass *Previous)
|
---|
775 | {
|
---|
776 | return false;
|
---|
777 | };
|
---|
778 |
|
---|
779 | /** Fills the root stack for sites to be used as root in fragmentation depending on order or adaptivity criteria
|
---|
780 | * Again, as in \sa FillBondStructureFromReference steps recursively through each Leaf in this chain list of molecule's.
|
---|
781 | * \param *out output stream for debugging
|
---|
782 | * \param *&RootStack stack to be filled
|
---|
783 | * \param *AtomMask defines true/false per global Atom::Nr to mask in/out each nuclear site
|
---|
784 | * \param &FragmentCounter counts through the fragments in this MoleculeLeafClass
|
---|
785 | * \return true - stack is non-empty, fragmentation necessary, false - stack is empty, no more sites to update
|
---|
786 | */
|
---|
787 | bool MoleculeLeafClass::FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter)
|
---|
788 | {
|
---|
789 | atom *Father = NULL;
|
---|
790 |
|
---|
791 | if (RootStack != NULL) {
|
---|
792 | // find first root candidates
|
---|
793 | if (&(RootStack[FragmentCounter]) != NULL) {
|
---|
794 | RootStack[FragmentCounter].clear();
|
---|
795 | for(molecule::const_iterator iter = Leaf->begin(); iter != Leaf->end(); ++iter) {
|
---|
796 | Father = (*iter)->GetTrueFather();
|
---|
797 | if (AtomMask[Father->getNr()]) // apply mask
|
---|
798 | #ifdef ADDHYDROGEN
|
---|
799 | if ((*iter)->getType()->getAtomicNumber() != 1) // skip hydrogen
|
---|
800 | #endif
|
---|
801 | RootStack[FragmentCounter].push_front((*iter)->getNr());
|
---|
802 | }
|
---|
803 | if (next != NULL)
|
---|
804 | next->FillRootStackForSubgraphs(RootStack, AtomMask, ++FragmentCounter);
|
---|
805 | } else {
|
---|
806 | DoLog(1) && (Log() << Verbose(1) << "Rootstack[" << FragmentCounter << "] is NULL." << endl);
|
---|
807 | return false;
|
---|
808 | }
|
---|
809 | FragmentCounter--;
|
---|
810 | return true;
|
---|
811 | } else {
|
---|
812 | DoLog(1) && (Log() << Verbose(1) << "Rootstack is NULL." << endl);
|
---|
813 | return false;
|
---|
814 | }
|
---|
815 | };
|
---|
816 |
|
---|
817 | /** The indices per keyset are compared to the respective father's Atom::Nr in each subgraph and thus put into \a **&FragmentList.
|
---|
818 | * \param *out output stream fro debugging
|
---|
819 | * \param *reference reference molecule with the bond structure to be copied
|
---|
820 | * \param *KeySetList list with all keysets
|
---|
821 | * \param ***ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
|
---|
822 | * \param **&FragmentList list to be allocated and returned
|
---|
823 | * \param &FragmentCounter counts the fragments as we move along the list
|
---|
824 | * \param FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
|
---|
825 | * \retuen true - success, false - failure
|
---|
826 | */
|
---|
827 | bool MoleculeLeafClass::AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList)
|
---|
828 | {
|
---|
829 | bool status = true;
|
---|
830 | int KeySetCounter = 0;
|
---|
831 |
|
---|
832 | DoLog(1) && (Log() << Verbose(1) << "Begin of AssignKeySetsToFragment." << endl);
|
---|
833 | // fill ListOfLocalAtoms if NULL was given
|
---|
834 | if (!Leaf->FillListOfLocalAtoms(ListOfLocalAtoms[FragmentCounter], reference->getAtomCount())) {
|
---|
835 | DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
|
---|
836 | return false;
|
---|
837 | }
|
---|
838 |
|
---|
839 | // allocate fragment list
|
---|
840 | if (FragmentList == NULL) {
|
---|
841 | KeySetCounter = Count();
|
---|
842 | FragmentList = new Graph*[KeySetCounter];
|
---|
843 | for (int i=0;i<KeySetCounter;i++)
|
---|
844 | FragmentList[i] = NULL;
|
---|
845 | KeySetCounter = 0;
|
---|
846 | }
|
---|
847 |
|
---|
848 | if ((KeySetList != NULL) && (KeySetList->size() != 0)) { // if there are some scanned keysets at all
|
---|
849 | // assign scanned keysets
|
---|
850 | if (FragmentList[FragmentCounter] == NULL)
|
---|
851 | FragmentList[FragmentCounter] = new Graph;
|
---|
852 | KeySet *TempSet = new KeySet;
|
---|
853 | for (Graph::iterator runner = KeySetList->begin(); runner != KeySetList->end(); runner++) { // key sets contain global numbers!
|
---|
854 | if (ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*((*runner).first.begin()))->getNr()] != NULL) {// as we may assume that that bond structure is unchanged, we only test the first key in each set
|
---|
855 | // translate keyset to local numbers
|
---|
856 | for (KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
|
---|
857 | TempSet->insert(ListOfLocalAtoms[FragmentCounter][reference->FindAtom(*sprinter)->getNr()]->getNr());
|
---|
858 | // insert into FragmentList
|
---|
859 | FragmentList[FragmentCounter]->insert(GraphPair(*TempSet, pair<int, double> (KeySetCounter++, (*runner).second.second)));
|
---|
860 | }
|
---|
861 | TempSet->clear();
|
---|
862 | }
|
---|
863 | delete (TempSet);
|
---|
864 | if (KeySetCounter == 0) {// if there are no keysets, delete the list
|
---|
865 | DoLog(1) && (Log() << Verbose(1) << "KeySetCounter is zero, deleting FragmentList." << endl);
|
---|
866 | delete (FragmentList[FragmentCounter]);
|
---|
867 | } else
|
---|
868 | DoLog(1) && (Log() << Verbose(1) << KeySetCounter << " keysets were assigned to subgraph " << FragmentCounter << "." << endl);
|
---|
869 | FragmentCounter++;
|
---|
870 | if (next != NULL)
|
---|
871 | next->AssignKeySetsToFragment(reference, KeySetList, ListOfLocalAtoms, FragmentList, FragmentCounter, FreeList);
|
---|
872 | FragmentCounter--;
|
---|
873 | } else
|
---|
874 | DoLog(1) && (Log() << Verbose(1) << "KeySetList is NULL or empty." << endl);
|
---|
875 |
|
---|
876 | if ((FreeList) && (ListOfLocalAtoms != NULL)) {
|
---|
877 | // free the index lookup list
|
---|
878 | delete[](ListOfLocalAtoms[FragmentCounter]);
|
---|
879 | }
|
---|
880 | DoLog(1) && (Log() << Verbose(1) << "End of AssignKeySetsToFragment." << endl);
|
---|
881 | return status;
|
---|
882 | };
|
---|
883 |
|
---|
884 | /** Translate list into global numbers (i.e. ones that are valid in "this" molecule, not in MolecularWalker->Leaf)
|
---|
885 | * \param *out output stream for debugging
|
---|
886 | * \param **FragmentList Graph with local numbers per fragment
|
---|
887 | * \param &FragmentCounter counts the fragments as we move along the list
|
---|
888 | * \param &TotalNumberOfKeySets global key set counter
|
---|
889 | * \param &TotalGraph Graph to be filled with global numbers
|
---|
890 | */
|
---|
891 | void MoleculeLeafClass::TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph)
|
---|
892 | {
|
---|
893 | DoLog(1) && (Log() << Verbose(1) << "Begin of TranslateIndicesToGlobalIDs." << endl);
|
---|
894 | KeySet *TempSet = new KeySet;
|
---|
895 | if (FragmentList[FragmentCounter] != NULL) {
|
---|
896 | for (Graph::iterator runner = FragmentList[FragmentCounter]->begin(); runner != FragmentList[FragmentCounter]->end(); runner++) {
|
---|
897 | for (KeySet::iterator sprinter = (*runner).first.begin(); sprinter != (*runner).first.end(); sprinter++)
|
---|
898 | TempSet->insert((Leaf->FindAtom(*sprinter))->GetTrueFather()->getNr());
|
---|
899 | TotalGraph.insert(GraphPair(*TempSet, pair<int, double> (TotalNumberOfKeySets++, (*runner).second.second)));
|
---|
900 | TempSet->clear();
|
---|
901 | }
|
---|
902 | delete (TempSet);
|
---|
903 | } else {
|
---|
904 | DoLog(1) && (Log() << Verbose(1) << "FragmentList is NULL." << endl);
|
---|
905 | }
|
---|
906 | if (next != NULL)
|
---|
907 | next->TranslateIndicesToGlobalIDs(FragmentList, ++FragmentCounter, TotalNumberOfKeySets, TotalGraph);
|
---|
908 | FragmentCounter--;
|
---|
909 | DoLog(1) && (Log() << Verbose(1) << "End of TranslateIndicesToGlobalIDs." << endl);
|
---|
910 | };
|
---|
911 |
|
---|
912 | /** Simply counts the number of items in the list, from given MoleculeLeafClass.
|
---|
913 | * \return number of items
|
---|
914 | */
|
---|
915 | int MoleculeLeafClass::Count() const
|
---|
916 | {
|
---|
917 | if (next != NULL)
|
---|
918 | return next->Count() + 1;
|
---|
919 | else
|
---|
920 | return 1;
|
---|
921 | };
|
---|
922 |
|
---|