1 | /** \file periodentafel.cpp
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2 | *
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3 | * Function implementations for the class periodentafel.
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4 | *
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5 | */
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6 |
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7 | using namespace std;
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8 |
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9 | #include <iomanip>
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10 | #include <iostream>
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11 | #include <fstream>
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12 | #include <cstring>
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13 |
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14 | #include "Helpers/Assert.hpp"
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15 | #include "element.hpp"
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16 | #include "elements_db.hpp"
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17 | #include "helpers.hpp"
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18 | #include "lists.hpp"
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19 | #include "log.hpp"
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20 | #include "periodentafel.hpp"
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21 | #include "verbose.hpp"
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22 |
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23 | using namespace std;
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24 |
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25 | /************************************* Functions for class periodentafel ***************************/
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26 |
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27 | /** constructor for class periodentafel
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28 | * Initialises start and end of list and resets periodentafel::checkliste to false.
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29 | */
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30 | periodentafel::periodentafel()
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31 | {
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32 | bool status = true;
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33 | status = LoadElementsDatabase(new stringstream(elementsDB,ios_base::in));
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34 | ASSERT(status, "General element initialization failed");
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35 | status = LoadValenceDatabase(new stringstream(valenceDB,ios_base::in));
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36 | ASSERT(status, "Valence entry of element initialization failed");
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37 | status = LoadOrbitalsDatabase(new stringstream(orbitalsDB,ios_base::in));
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38 | ASSERT(status, "Orbitals entry of element initialization failed");
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39 | status = LoadHBondAngleDatabase(new stringstream(HbondangleDB,ios_base::in));
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40 | ASSERT(status, "HBond angle entry of element initialization failed");
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41 | status = LoadHBondLengthsDatabase(new stringstream(HbonddistanceDB,ios_base::in));
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42 | ASSERT(status, "HBond distance entry of element initialization failed");
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43 | };
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44 |
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45 | /** destructor for class periodentafel
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46 | * Removes every element and afterwards deletes start and end of list.
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47 | * TODO: Handle when elements have changed and store databases then
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48 | */
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49 | periodentafel::~periodentafel()
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50 | {
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51 | CleanupPeriodtable();
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52 | };
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53 |
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54 | /** Adds element to period table list
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55 | * \param *pointer element to be added
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56 | * \return iterator to added element
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57 | */
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58 | periodentafel::iterator periodentafel::AddElement(element * const pointer)
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59 | {
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60 | atomicNumber_t Z = pointer->getNumber();
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61 | ASSERT(!elements.count(Z), "Element is already present.");
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62 | pointer->sort = &pointer->Z;
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63 | if (pointer->getNumber() < 1 && pointer->getNumber() >= MAX_ELEMENTS)
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64 | DoeLog(0) && (eLog() << Verbose(0) << "Invalid Z number!\n");
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65 | pair<iterator,bool> res = elements.insert(pair<atomicNumber_t,element*>(Z,pointer));
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66 | return res.first;
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67 | };
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68 |
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69 | /** Removes element from list.
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70 | * \param *pointer element to be removed
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71 | */
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72 | size_t periodentafel::RemoveElement(element * const pointer)
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73 | {
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74 | return RemoveElement(pointer->getNumber());
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75 | };
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76 |
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77 | /** Removes element from list.
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78 | * \param Z element to be removed
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79 | */
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80 | size_t periodentafel::RemoveElement(atomicNumber_t Z)
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81 | {
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82 | return elements.erase(Z);
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83 | };
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84 |
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85 | /** Removes every element from the period table.
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86 | */
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87 | void periodentafel::CleanupPeriodtable()
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88 | {
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89 | for(iterator iter=elements.begin();iter!=elements.end();++iter){
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90 | delete(*iter).second;
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91 | }
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92 | elements.clear();
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93 | };
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94 |
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95 | /** Finds an element by its atomic number.
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96 | * If element is not yet in list, returns NULL.
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97 | * \param Z atomic number
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98 | * \return pointer to element or NULL if not found
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99 | */
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100 | element * const periodentafel::FindElement(atomicNumber_t Z) const
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101 | {
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102 | const_iterator res = elements.find(Z);
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103 | return res!=elements.end()?((*res).second):0;
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104 | };
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105 |
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106 | /** Finds an element by its atomic number.
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107 | * If element is not yet in list, datas are asked and stored in database.
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108 | * \param shorthand chemical symbol of the element, e.g. H for hydrogene
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109 | * \return pointer to element
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110 | */
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111 | element * const periodentafel::FindElement(const char * const shorthand) const
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112 | {
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113 | element *res = 0;
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114 | for(const_iterator iter=elements.begin();iter!=elements.end();++iter) {
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115 | if((*iter).second->getSymbol() == shorthand){
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116 | res = (*iter).second;
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117 | break;
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118 | }
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119 | }
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120 | return res;
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121 | };
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122 |
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123 | /** Asks for element number and returns pointer to element
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124 | * \return desired element or NULL
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125 | */
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126 | element * const periodentafel::AskElement() const
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127 | {
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128 | element * walker = NULL;
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129 | int Z;
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130 | do {
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131 | DoLog(0) && (Log() << Verbose(0) << "Atomic number Z: ");
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132 | cin >> Z;
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133 | walker = this->FindElement(Z); // give type
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134 | } while (walker == NULL);
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135 | return walker;
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136 | };
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137 |
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138 | /** Asks for element and if not found, presents mask to enter info.
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139 | * \return pointer to either present or newly created element
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140 | */
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141 | element * const periodentafel::EnterElement()
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142 | {
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143 | atomicNumber_t Z = 0;
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144 | DoLog(0) && (Log() << Verbose(0) << "Atomic number: " << Z << endl);
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145 | cin >> Z;
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146 | element * const res = FindElement(Z);
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147 | if (!res) {
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148 | // TODO: make this using the constructor
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149 | DoLog(0) && (Log() << Verbose(0) << "Element not found in database, please enter." << endl);
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150 | element *tmp = new element;
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151 | tmp->Z = Z;
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152 | DoLog(0) && (Log() << Verbose(0) << "Mass: " << endl);
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153 | cin >> tmp->mass;
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154 | DoLog(0) && (Log() << Verbose(0) << "Name [max 64 chars]: " << endl);
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155 | cin >> tmp->name;
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156 | DoLog(0) && (Log() << Verbose(0) << "Short form [max 3 chars]: " << endl);
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157 | cin >> tmp->symbol;
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158 | AddElement(tmp);
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159 | return tmp;
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160 | }
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161 | return res;
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162 | };
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163 |
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164 |
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165 | /******************** Access to iterators ****************************/
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166 | periodentafel::const_iterator periodentafel::begin(){
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167 | return elements.begin();
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168 | }
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169 |
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170 | periodentafel::const_iterator periodentafel::end(){
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171 | return elements.end();
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172 | }
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173 |
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174 | periodentafel::reverse_iterator periodentafel::rbegin(){
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175 | return reverse_iterator(elements.end());
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176 | }
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177 |
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178 | periodentafel::reverse_iterator periodentafel::rend(){
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179 | return reverse_iterator(elements.begin());
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180 | }
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181 |
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182 | /** Prints period table to given stream.
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183 | * \param output stream
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184 | */
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185 | bool periodentafel::Output(ostream * const output) const
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186 | {
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187 | bool result = true;
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188 | if (output != NULL) {
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189 | for(const_iterator iter=elements.begin(); iter !=elements.end();++iter){
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190 | result = result && (*iter).second->Output(output);
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191 | }
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192 | return result;
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193 | } else
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194 | return false;
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195 | };
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196 |
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197 | /** Prints period table to given stream.
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198 | * \param *output output stream
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199 | * \param *checkliste elements table for this molecule
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200 | */
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201 | bool periodentafel::Checkout(ostream * const output, const int * const checkliste) const
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202 | {
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203 | bool result = true;
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204 | int No = 1;
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205 |
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206 | if (output != NULL) {
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207 | *output << "# Ion type data (PP = PseudoPotential, Z = atomic number)" << endl;
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208 | *output << "#Ion_TypeNr.\tAmount\tZ\tRGauss\tL_Max(PP)L_Loc(PP)IonMass\t# chemical name, symbol" << endl;
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209 | for(const_iterator iter=elements.begin(); iter!=elements.end();++iter){
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210 | if (((*iter).first < MAX_ELEMENTS) && (checkliste[(*iter).first])) {
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211 | (*iter).second->No = No;
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212 | result = result && (*iter).second->Checkout(output, No++, checkliste[(*iter).first]);
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213 | }
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214 | }
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215 | return result;
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216 | } else
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217 | return false;
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218 | };
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219 |
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220 | /** Loads element list from file.
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221 | * \param *path to to standard file names
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222 | */
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223 | bool periodentafel::LoadPeriodentafel(const char *path)
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224 | {
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225 | ifstream input;
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226 | bool status = true;
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227 | bool otherstatus = true;
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228 | char filename[255];
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229 |
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230 | // fill elements DB
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231 | strncpy(filename, path, MAXSTRINGSIZE);
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232 | strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
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233 | strncat(filename, STANDARDELEMENTSDB, MAXSTRINGSIZE-strlen(filename));
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234 | input.open(filename);
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235 | if (!input.fail())
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236 | DoLog(0) && (Log() << Verbose(0) << "Using " << filename << " as elements database." << endl);
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237 | status = status && LoadElementsDatabase(&input);
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238 | input.close();
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239 | input.clear();
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240 |
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241 | // fill valence DB per element
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242 | strncpy(filename, path, MAXSTRINGSIZE);
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243 | strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
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244 | strncat(filename, STANDARDVALENCEDB, MAXSTRINGSIZE-strlen(filename));
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245 | input.open(filename);
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246 | if (!input.fail())
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247 | DoLog(0) && (Log() << Verbose(0) << "Using " << filename << " as valence database." << endl);
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248 | otherstatus = otherstatus && LoadValenceDatabase(&input);
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249 | input.close();
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250 | input.clear();
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251 |
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252 | // fill orbitals DB per element
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253 | strncpy(filename, path, MAXSTRINGSIZE);
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254 | strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
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255 | strncat(filename, STANDARDORBITALDB, MAXSTRINGSIZE-strlen(filename));
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256 | input.open(filename);
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257 | if (!input.fail())
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258 | DoLog(0) && (Log() << Verbose(0) << "Using " << filename << " as orbitals database." << endl);
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259 | otherstatus = otherstatus && LoadOrbitalsDatabase(&input);
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260 | input.close();
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261 | input.clear();
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262 |
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263 | // fill H-BondAngle DB per element
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264 | strncpy(filename, path, MAXSTRINGSIZE);
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265 | strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
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266 | strncat(filename, STANDARDHBONDANGLEDB, MAXSTRINGSIZE-strlen(filename));
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267 | input.open(filename);
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268 | if (!input.fail())
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269 | DoLog(0) && (Log() << Verbose(0) << "Using " << filename << " as H bond angle database." << endl);
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270 | otherstatus = otherstatus && LoadHBondAngleDatabase(&input);
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271 | input.close();
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272 | input.clear();
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273 |
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274 | // fill H-BondDistance DB per element
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275 | strncpy(filename, path, MAXSTRINGSIZE);
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276 | strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
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277 | strncat(filename, STANDARDHBONDDISTANCEDB, MAXSTRINGSIZE-strlen(filename));
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278 | input.open(filename);
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279 | if (!input.fail())
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280 | DoLog(0) && (Log() << Verbose(0) << "Using " << filename << " as H bond length database." << endl);
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281 | otherstatus = otherstatus && LoadHBondLengthsDatabase(&input);
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282 | input.close();
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283 | input.clear();
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284 |
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285 | if (!otherstatus){
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286 | DoeLog(2) && (eLog()<< Verbose(2) << "Something went wrong while parsing the other databases!" << endl);
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287 | }
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288 |
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289 | return status;
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290 | };
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291 |
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292 | /** load the element info.
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293 | * \param *input stream to parse from
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294 | * \return true - parsing successful, false - something went wrong
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295 | */
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296 | bool periodentafel::LoadElementsDatabase(istream *input)
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297 | {
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298 | bool status = true;
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299 | int counter = 0;
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300 | pair< std::map<atomicNumber_t,element*>::iterator, bool > InserterTest;
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301 | if (!(*input).fail()) {
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302 | (*input).getline(header1, MAXSTRINGSIZE);
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303 | (*input).getline(header2, MAXSTRINGSIZE); // skip first two header lines
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304 | DoLog(0) && (Log() << Verbose(0) << "Parsed elements:");
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305 | while (!(*input).eof()) {
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306 | element *neues = new element;
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307 | (*input) >> neues->name;
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308 | //(*input) >> ws;
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309 | (*input) >> neues->symbol;
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310 | //(*input) >> ws;
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311 | (*input) >> neues->period;
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312 | //(*input) >> ws;
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313 | (*input) >> neues->group;
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314 | //(*input) >> ws;
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315 | (*input) >> neues->block;
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316 | //(*input) >> ws;
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317 | (*input) >> neues->Z;
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318 | //(*input) >> ws;
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319 | (*input) >> neues->mass;
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320 | //(*input) >> ws;
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321 | (*input) >> neues->CovalentRadius;
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322 | //(*input) >> ws;
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323 | (*input) >> neues->VanDerWaalsRadius;
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324 | //(*input) >> ws;
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325 | (*input) >> ws;
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326 | //neues->Output((ofstream *)&cout);
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327 | if ((neues->getNumber() > 0) && (neues->getNumber() < MAX_ELEMENTS)) {
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328 | if (elements.count(neues->getNumber())) {// if element already present, remove and delete old one (i.e. replace it)
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329 | //cout << neues->symbol << " is present already." << endl;
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330 | element * const Elemental = FindElement(neues->getNumber());
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331 | ASSERT(Elemental != NULL, "element should be present but is not??");
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332 | *Elemental = *neues;
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333 | } else {
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334 | InserterTest = elements.insert(pair <atomicNumber_t,element*> (neues->getNumber(), neues));
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335 | ASSERT(InserterTest.second, "Could not insert new element into periodentafel on LoadElementsDatabase().");
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336 | }
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337 | DoLog(0) && (Log() << Verbose(0) << " " << elements[neues->getNumber()]->symbol);
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338 | counter++;
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339 | } else {
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340 | DoeLog(2) && (eLog() << Verbose(2) << "Detected empty line or invalid element in elements db, discarding." << endl);
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341 | DoLog(0) && (Log() << Verbose(0) << " <?>");
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342 | delete(neues);
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343 | }
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344 | }
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345 | DoLog(0) && (Log() << Verbose(0) << endl);
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346 | } else {
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347 | DoeLog(1) && (eLog() << Verbose(1) << "Could not open the database." << endl);
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348 | status = false;
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349 | }
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350 |
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351 | if (counter == 0)
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352 | status = false;
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353 |
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354 | return status;
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355 | }
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356 |
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357 | /** load the valence info.
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358 | * \param *input stream to parse from
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359 | * \return true - parsing successful, false - something went wrong
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360 | */
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361 | bool periodentafel::LoadValenceDatabase(istream *input)
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362 | {
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363 | char dummy[MAXSTRINGSIZE];
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364 | if (!(*input).fail()) {
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365 | (*input).getline(dummy, MAXSTRINGSIZE);
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366 | while (!(*input).eof()) {
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367 | atomicNumber_t Z;
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368 | (*input) >> Z;
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369 | ASSERT(elements.count(Z), "Element not present");
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370 | (*input) >> ws;
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371 | (*input) >> elements[Z]->Valence;
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372 | (*input) >> ws;
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373 | //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->Valence << " valence electrons." << endl;
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374 | }
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375 | return true;
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376 | } else
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377 | return false;
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378 | }
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379 |
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380 | /** load the orbitals info.
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381 | * \param *input stream to parse from
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382 | * \return true - parsing successful, false - something went wrong
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383 | */
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384 | bool periodentafel::LoadOrbitalsDatabase(istream *input)
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385 | {
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386 | char dummy[MAXSTRINGSIZE];
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387 | if (!(*input).fail()) {
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388 | (*input).getline(dummy, MAXSTRINGSIZE);
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389 | while (!(*input).eof()) {
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390 | atomicNumber_t Z;
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391 | (*input) >> Z;
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392 | ASSERT(elements.count(Z), "Element not present");
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393 | (*input) >> ws;
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394 | (*input) >> elements[Z]->NoValenceOrbitals;
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395 | (*input) >> ws;
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396 | //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->NoValenceOrbitals << " number of singly occupied valence orbitals." << endl;
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397 | }
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398 | return true;
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399 | } else
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400 | return false;
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401 | }
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402 |
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403 | /** load the hbond angles info.
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404 | * \param *input stream to parse from
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405 | * \return true - parsing successful, false - something went wrong
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406 | */
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407 | bool periodentafel::LoadHBondAngleDatabase(istream *input)
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408 | {
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409 | char dummy[MAXSTRINGSIZE];
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410 | if (!(*input).fail()) {
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411 | (*input).getline(dummy, MAXSTRINGSIZE);
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412 | while (!(*input).eof()) {
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413 | atomicNumber_t Z;
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414 | (*input) >> Z;
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415 | ASSERT(elements.count(Z), "Element not present");
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416 | (*input) >> ws;
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417 | (*input) >> elements[Z]->HBondAngle[0];
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418 | (*input) >> elements[Z]->HBondAngle[1];
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419 | (*input) >> elements[Z]->HBondAngle[2];
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420 | (*input) >> ws;
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421 | //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->HBondAngle[0] << ", " << FindElement((int)tmp)->HBondAngle[1] << ", " << FindElement((int)tmp)->HBondAngle[2] << " degrees bond angle for one, two, three connected hydrogens." << endl;
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422 | }
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423 | return true;
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424 | } else
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425 | return false;
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426 | }
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427 |
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428 | /** load the hbond lengths info.
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429 | * \param *input stream to parse from
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430 | * \return true - parsing successful, false - something went wrong
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431 | */
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432 | bool periodentafel::LoadHBondLengthsDatabase(istream *input)
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433 | {
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434 | char dummy[MAXSTRINGSIZE];
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435 | if (!(*input).fail()) {
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436 | (*input).getline(dummy, MAXSTRINGSIZE);
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437 | while (!(*input).eof()) {
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438 | atomicNumber_t Z;
|
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439 | (*input) >> Z;
|
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440 | ASSERT(elements.count(Z), "Element not present");
|
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441 | (*input) >> ws;
|
---|
442 | (*input) >> elements[Z]->HBondDistance[0];
|
---|
443 | (*input) >> elements[Z]->HBondDistance[1];
|
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444 | (*input) >> elements[Z]->HBondDistance[2];
|
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445 | (*input) >> ws;
|
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446 | //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->HBondDistance[0] << " Angstrom typical distance to hydrogen." << endl;
|
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447 | }
|
---|
448 | return true;
|
---|
449 | } else
|
---|
450 | return false;
|
---|
451 | }
|
---|
452 |
|
---|
453 | /** Stores element list to file.
|
---|
454 | */
|
---|
455 | bool periodentafel::StorePeriodentafel(const char *path) const
|
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456 | {
|
---|
457 | bool result = true;
|
---|
458 | ofstream f;
|
---|
459 | char filename[MAXSTRINGSIZE];
|
---|
460 |
|
---|
461 | strncpy(filename, path, MAXSTRINGSIZE);
|
---|
462 | strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
|
---|
463 | strncat(filename, STANDARDELEMENTSDB, MAXSTRINGSIZE-strlen(filename));
|
---|
464 | f.open(filename);
|
---|
465 | if (f != NULL) {
|
---|
466 | f << header1 << endl;
|
---|
467 | f << header2 << endl;
|
---|
468 | for(const_iterator iter=elements.begin();iter!=elements.end();++iter){
|
---|
469 | result = result && (*iter).second->Output(&f);
|
---|
470 | }
|
---|
471 | f.close();
|
---|
472 | return true;
|
---|
473 | } else
|
---|
474 | return result;
|
---|
475 | };
|
---|