1 | /*
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2 | * Project: MoleCuilder
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3 | * Description: creates and alters molecular systems
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4 | * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
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5 | * 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 <iostream>
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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 "MoleculeListClass.hpp"
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27 |
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28 | #include "CodePatterns/Log.hpp"
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29 |
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30 | #include "Atom/atom.hpp"
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31 | #include "Bond/bond.hpp"
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32 | #include "Box.hpp"
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33 | #include "config.hpp"
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34 | #include "Element/element.hpp"
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35 | #include "Element/periodentafel.hpp"
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36 | #include "Fragmentation/Graph.hpp"
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37 | #include "Fragmentation/KeySet.hpp"
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38 | #include "Graph/BondGraph.hpp"
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39 | #include "Helpers/helpers.hpp"
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40 | #include "molecule.hpp"
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41 | #include "LinearAlgebra/RealSpaceMatrix.hpp"
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42 | #include "Parser/FormatParserStorage.hpp"
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43 | #include "World.hpp"
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44 |
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45 |
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46 | /** Constructor for MoleculeListClass.
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47 | */
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48 | MoleculeListClass::MoleculeListClass(World *_world) :
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49 | Observable("MoleculeListClass"),
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50 | MaxIndex(1),
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51 | world(_world)
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52 | {};
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53 |
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54 | /** Destructor for MoleculeListClass.
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55 | */
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56 | MoleculeListClass::~MoleculeListClass()
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57 | {
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58 | LOG(4, "Clearing ListOfMolecules.");
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59 | for(MoleculeList::iterator MolRunner = ListOfMolecules.begin(); MolRunner != ListOfMolecules.end(); ++MolRunner)
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60 | (*MolRunner)->signOff(this);
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61 | ListOfMolecules.clear(); // empty list
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62 | };
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63 |
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64 | /** Insert a new molecule into the list and set its number.
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65 | * \param *mol molecule to add to list.
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66 | */
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67 | void MoleculeListClass::insert(molecule *mol)
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68 | {
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69 | OBSERVE;
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70 | mol->IndexNr = MaxIndex++;
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71 | ListOfMolecules.push_back(mol);
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72 | mol->signOn(this);
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73 | };
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74 |
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75 | /** Erases a molecule from the list.
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76 | * \param *mol molecule to add to list.
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77 | */
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78 | void MoleculeListClass::erase(molecule *mol)
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79 | {
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80 | OBSERVE;
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81 | mol->signOff(this);
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82 | ListOfMolecules.remove(mol);
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83 | };
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84 |
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85 | /** Comparison function for two values.
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86 | * \param *a
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87 | * \param *b
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88 | * \return <0, \a *a less than \a *b, ==0 if equal, >0 \a *a greater than \a *b
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89 | */
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90 | int CompareDoubles (const void * a, const void * b)
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91 | {
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92 | if (*(double *)a > *(double *)b)
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93 | return -1;
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94 | else if (*(double *)a < *(double *)b)
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95 | return 1;
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96 | else
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97 | return 0;
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98 | };
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99 |
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100 |
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101 | /** Compare whether two molecules are equal.
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102 | * \param *a molecule one
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103 | * \param *n molecule two
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104 | * \return lexical value (-1, 0, +1)
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105 | */
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106 | int MolCompare(const void *a, const void *b)
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107 | {
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108 | int *aList = NULL, *bList = NULL;
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109 | int Count, Counter, aCounter, bCounter;
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110 | int flag;
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111 |
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112 | // sort each atom list and put the numbers into a list, then go through
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113 | //LOG(0, "Comparing fragment no. " << *(molecule **)a << " to " << *(molecule **)b << ".");
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114 | // Yes those types are awkward... but check it for yourself it checks out this way
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115 | molecule *const *mol1_ptr= static_cast<molecule *const *>(a);
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116 | molecule *mol1 = *mol1_ptr;
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117 | molecule *const *mol2_ptr= static_cast<molecule *const *>(b);
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118 | molecule *mol2 = *mol2_ptr;
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119 | if (mol1->getAtomCount() < mol2->getAtomCount()) {
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120 | return -1;
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121 | } else {
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122 | if (mol1->getAtomCount() > mol2->getAtomCount())
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123 | return +1;
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124 | else {
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125 | Count = mol1->getAtomCount();
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126 | aList = new int[Count];
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127 | bList = new int[Count];
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128 |
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129 | // fill the lists
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130 | Counter = 0;
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131 | aCounter = 0;
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132 | bCounter = 0;
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133 | molecule::const_iterator aiter = mol1->begin();
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134 | molecule::const_iterator biter = mol2->begin();
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135 | for (;(aiter != mol1->end()) && (biter != mol2->end());
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136 | ++aiter, ++biter) {
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137 | if ((*aiter)->GetTrueFather() == NULL)
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138 | aList[Counter] = Count + (aCounter++);
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139 | else
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140 | aList[Counter] = (*aiter)->GetTrueFather()->getNr();
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141 | if ((*biter)->GetTrueFather() == NULL)
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142 | bList[Counter] = Count + (bCounter++);
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143 | else
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144 | bList[Counter] = (*biter)->GetTrueFather()->getNr();
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145 | Counter++;
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146 | }
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147 | // check if AtomCount was for real
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148 | flag = 0;
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149 | if ((aiter == mol1->end()) && (biter != mol2->end())) {
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150 | flag = -1;
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151 | } else {
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152 | if ((aiter != mol1->end()) && (biter == mol2->end()))
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153 | flag = 1;
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154 | }
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155 | if (flag == 0) {
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156 | // sort the lists
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157 | gsl_heapsort(aList, Count, sizeof(int), CompareDoubles);
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158 | gsl_heapsort(bList, Count, sizeof(int), CompareDoubles);
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159 | // compare the lists
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160 |
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161 | flag = 0;
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162 | for (int i = 0; i < Count; i++) {
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163 | if (aList[i] < bList[i]) {
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164 | flag = -1;
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165 | } else {
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166 | if (aList[i] > bList[i])
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167 | flag = 1;
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168 | }
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169 | if (flag != 0)
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170 | break;
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171 | }
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172 | }
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173 | delete[] (aList);
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174 | delete[] (bList);
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175 | return flag;
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176 | }
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177 | }
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178 | return -1;
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179 | };
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180 |
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181 | /** Output of a list of all molecules.
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182 | * \param *out output stream
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183 | */
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184 | void MoleculeListClass::Enumerate(std::ostream *out)
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185 | {
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186 | periodentafel *periode = World::getInstance().getPeriode();
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187 | std::map<atomicNumber_t,unsigned int> counts;
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188 | double size=0;
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189 | Vector Origin;
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190 |
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191 | // header
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192 | (*out) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
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193 | (*out) << "-----------------------------------------------" << endl;
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194 | if (ListOfMolecules.size() == 0)
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195 | (*out) << "\tNone" << endl;
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196 | else {
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197 | Origin.Zero();
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198 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
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199 | // count atoms per element and determine size of bounding sphere
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200 | size=0.;
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201 | for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
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202 | counts[(*iter)->getType()->getNumber()]++;
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203 | if ((*iter)->DistanceSquared(Origin) > size)
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204 | size = (*iter)->DistanceSquared(Origin);
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205 | }
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206 | // output Index, Name, number of atoms, chemical formula
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207 | (*out) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->getAtomCount() << "\t";
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208 |
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209 | std::map<atomicNumber_t,unsigned int>::reverse_iterator iter;
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210 | for(iter=counts.rbegin(); iter!=counts.rend();++iter){
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211 | atomicNumber_t Z =(*iter).first;
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212 | (*out) << periode->FindElement(Z)->getSymbol() << (*iter).second;
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213 | }
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214 | // Center and size
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215 | Vector *Center = (*ListRunner)->DetermineCenterOfAll();
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216 | (*out) << "\t" << *Center << "\t" << sqrt(size) << endl;
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217 | delete(Center);
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218 | }
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219 | }
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220 | };
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221 |
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222 | /** Returns the molecule with the given index \a index.
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223 | * \param index index of the desired molecule
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224 | * \return pointer to molecule structure, NULL if not found
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225 | */
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226 | molecule * MoleculeListClass::ReturnIndex(int index)
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227 | {
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228 | for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
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229 | if ((*ListRunner)->IndexNr == index)
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230 | return (*ListRunner);
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231 | return NULL;
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232 | };
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233 |
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234 |
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235 | /** Simple output of the pointers in ListOfMolecules.
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236 | * \param *out output stream
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237 | */
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238 | void MoleculeListClass::Output(std::ostream *out)
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239 | {
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240 | if (DoLog(1)) {
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241 | std::stringstream output;
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242 | output << "MoleculeList: ";
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243 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
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244 | output << *ListRunner << "\t";
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245 | LOG(1, output.str());
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246 | }
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247 | };
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248 |
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249 | /** Returns a string with \a i prefixed with 0s to match order of total number of molecules in digits.
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250 | * \param FragmentNumber total number of fragments to determine necessary number of digits
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251 | * \param digits number to create with 0 prefixed
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252 | * \return allocated(!) char array with number in digits, ten base.
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253 | */
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254 | inline char *FixedDigitNumber(const int FragmentNumber, const int digits)
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255 | {
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256 | char *returnstring;
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257 | int number = FragmentNumber;
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258 | int order = 0;
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259 | while (number != 0) { // determine number of digits needed
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260 | number = (int)floor(((double)number / 10.));
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261 | order++;
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262 | //LOG(0, "Number is " << number << ", order is " << order << ".");
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263 | }
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264 | // allocate string
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265 | returnstring = new char[order + 2];
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266 | // terminate and fill string array from end backward
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267 | returnstring[order] = '\0';
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268 | number = digits;
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269 | for (int i=order;i--;) {
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270 | returnstring[i] = '0' + (char)(number % 10);
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271 | number = (int)floor(((double)number / 10.));
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272 | }
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273 | //LOG(0, returnstring);
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274 | return returnstring;
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275 | };
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276 |
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277 | /** Calculates necessary hydrogen correction due to unwanted interaction between saturated ones.
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278 | * 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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279 | * bonded to the same atom, then we add for this pair a correction term constructed from a Morse
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280 | * potential function fit to QM calculations with respecting to the interatomic hydrogen distance.
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281 | * \param &path path to file
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282 | */
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283 | bool MoleculeListClass::AddHydrogenCorrection(std::string &path)
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284 | {
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285 | const bond *Binder = NULL;
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286 | double ***FitConstant = NULL, **correction = NULL;
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287 | int a, b;
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288 | ofstream output;
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289 | ifstream input;
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290 | string line;
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291 | stringstream zeile;
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292 | double distance;
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293 | char ParsedLine[1023];
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294 | double tmp;
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295 | char *FragmentNumber = NULL;
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296 |
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297 | LOG(1, "Saving hydrogen saturation correction ... ");
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298 | // 0. parse in fit constant files that should have the same dimension as the final energy files
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299 | // 0a. find dimension of matrices with constants
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300 | line = path;
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301 | line += "1";
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302 | line += FITCONSTANTSUFFIX;
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303 | input.open(line.c_str());
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304 | if (input.fail()) {
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305 | LOG(1, endl << "Unable to open " << line << ", is the directory correct?");
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306 | return false;
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307 | }
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308 | a = 0;
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309 | b = -1; // we overcount by one
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310 | while (!input.eof()) {
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311 | input.getline(ParsedLine, 1023);
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312 | zeile.str(ParsedLine);
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313 | int i = 0;
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314 | while (!zeile.eof()) {
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315 | zeile >> distance;
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316 | i++;
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317 | }
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318 | if (i > a)
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319 | a = i;
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320 | b++;
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321 | }
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322 | LOG(0, "I recognized " << a << " columns and " << b << " rows, ");
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323 | input.close();
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324 |
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325 | // 0b. allocate memory for constants
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326 | FitConstant = new double**[3];
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327 | for (int k = 0; k < 3; k++) {
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328 | FitConstant[k] = new double*[a];
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329 | for (int i = a; i--;) {
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330 | FitConstant[k][i] = new double[b];
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331 | for (int j = b; j--;) {
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332 | FitConstant[k][i][j] = 0.;
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333 | }
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334 | }
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335 | }
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336 | // 0c. parse in constants
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337 | for (int i = 0; i < 3; i++) {
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338 | line = path;
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339 | line.append("/");
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340 | line += FRAGMENTPREFIX;
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341 | sprintf(ParsedLine, "%d", i + 1);
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342 | line += ParsedLine;
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343 | line += FITCONSTANTSUFFIX;
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344 | input.open(line.c_str());
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345 | if (input.fail()) {
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346 | ELOG(0, endl << "Unable to open " << line << ", is the directory correct?");
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347 | performCriticalExit();
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348 | return false;
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349 | }
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350 | int k = 0, l;
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351 | while ((!input.eof()) && (k < b)) {
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352 | input.getline(ParsedLine, 1023);
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353 | //LOG(1, "INFO: Current Line: " << ParsedLine);
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354 | zeile.str(ParsedLine);
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355 | zeile.clear();
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356 | l = 0;
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357 | //std::stringstream output;
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358 | while ((!zeile.eof()) && (l < a)) {
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359 | zeile >> FitConstant[i][l][k];
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360 | //output << FitConstant[i][l][k] << "\t";
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361 | l++;
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362 | }
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363 | //LOG(1, "INFO: fit constant are " << output.str());
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364 | k++;
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365 | }
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366 | input.close();
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367 | }
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368 | if (DoLog(1)) {
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369 | for (int k = 0; k < 3; k++) {
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370 | std::stringstream output;
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371 | output << "Constants " << k << ": ";
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372 | for (int j = 0; j < b; j++) {
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373 | for (int i = 0; i < a; i++) {
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374 | output << FitConstant[k][i][j] << "\t";
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375 | }
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376 | output << std::endl;
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377 | }
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378 | LOG(0, output.str());
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379 | }
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380 | }
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381 |
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382 | // 0d. allocate final correction matrix
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383 | correction = new double*[a];
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384 | for (int i = a; i--;)
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385 | correction[i] = new double[b];
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386 |
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387 | // 1a. go through every molecule in the list
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388 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
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389 | // 1b. zero final correction matrix
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390 | for (int k = a; k--;)
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391 | for (int j = b; j--;)
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392 | correction[k][j] = 0.;
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393 | // 2. take every hydrogen that is a saturated one
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394 | for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
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395 | //LOG(1, "(*iter): " << *(*iter) << " with first bond " << *((*iter)->getListOfBonds().begin()) << ".");
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396 | if (((*iter)->getType()->getAtomicNumber() == 1) && (((*iter)->father == NULL)
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397 | || ((*iter)->father->getType()->getAtomicNumber() != 1))) { // if it's a hydrogen
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398 | for (molecule::const_iterator runner = (*ListRunner)->begin(); runner != (*ListRunner)->end(); ++runner) {
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399 | //LOG(2, "Runner: " << *(*runner) << " with first bond " << *((*iter)->getListOfBonds().begin()) << ".");
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400 | // 3. take every other hydrogen that is the not the first and not bound to same bonding partner
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401 | const BondList &bondlist = (*runner)->getListOfBonds();
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402 | Binder = *(bondlist.begin());
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403 | 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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404 | // 4. evaluate the morse potential for each matrix component and add up
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405 | distance = (*runner)->distance(*(*iter));
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406 | //std::stringstream output;
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407 | //output << "Fragment " << (*ListRunner)->name << ": " << *(*runner) << "<= " << distance << "=>" << *(*iter) << ":";
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408 | for (int k = 0; k < a; k++) {
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409 | for (int j = 0; j < b; j++) {
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410 | switch (k) {
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411 | case 1:
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412 | case 7:
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413 | case 11:
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414 | tmp = pow(FitConstant[0][k][j] * (1. - exp(-FitConstant[1][k][j] * (distance - FitConstant[2][k][j]))), 2);
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415 | break;
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416 | default:
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417 | tmp = FitConstant[0][k][j] * pow(distance, FitConstant[1][k][j]) + FitConstant[2][k][j];
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418 | break;
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419 | };
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420 | correction[k][j] -= tmp; // ground state is actually lower (disturbed by additional interaction)
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421 | //output << tmp << "\t";
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422 | }
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423 | //output << endl;
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424 | }
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425 | //LOG(0, output.str());
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426 | }
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427 | }
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428 | }
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429 | }
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430 | // 5. write final matrix to file
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431 | line = path;
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432 | line.append("/");
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433 | line += FRAGMENTPREFIX;
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434 | FragmentNumber = FixedDigitNumber(ListOfMolecules.size(), (*ListRunner)->IndexNr);
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435 | line += FragmentNumber;
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436 | delete[] (FragmentNumber);
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437 | line += HCORRECTIONSUFFIX;
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438 | output.open(line.c_str());
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439 | output << "Time\t\tTotal\t\tKinetic\t\tNonLocal\tCorrelation\tExchange\tPseudo\t\tHartree\t\t-Gauss\t\tEwald\t\tIonKin\t\tETotal" << endl;
|
---|
440 | for (int j = 0; j < b; j++) {
|
---|
441 | for (int i = 0; i < a; i++)
|
---|
442 | output << correction[i][j] << "\t";
|
---|
443 | output << endl;
|
---|
444 | }
|
---|
445 | output.close();
|
---|
446 | }
|
---|
447 | for (int i = a; i--;)
|
---|
448 | delete[](correction[i]);
|
---|
449 | delete[](correction);
|
---|
450 |
|
---|
451 | line = path;
|
---|
452 | line.append("/");
|
---|
453 | line += HCORRECTIONSUFFIX;
|
---|
454 | output.open(line.c_str());
|
---|
455 | output << "Time\t\tTotal\t\tKinetic\t\tNonLocal\tCorrelation\tExchange\tPseudo\t\tHartree\t\t-Gauss\t\tEwald\t\tIonKin\t\tETotal" << endl;
|
---|
456 | for (int j = 0; j < b; j++) {
|
---|
457 | for (int i = 0; i < a; i++)
|
---|
458 | output << 0 << "\t";
|
---|
459 | output << endl;
|
---|
460 | }
|
---|
461 | output.close();
|
---|
462 | // 6. free memory of parsed matrices
|
---|
463 | for (int k = 0; k < 3; k++) {
|
---|
464 | for (int i = a; i--;) {
|
---|
465 | delete[](FitConstant[k][i]);
|
---|
466 | }
|
---|
467 | delete[](FitConstant[k]);
|
---|
468 | }
|
---|
469 | delete[](FitConstant);
|
---|
470 | LOG(0, "done.");
|
---|
471 | return true;
|
---|
472 | };
|
---|
473 |
|
---|
474 | /** Store force indices, i.e. the connection between the nuclear index in the total molecule config and the respective atom in fragment config.
|
---|
475 | * \param &path path to file
|
---|
476 | * \param *SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
|
---|
477 | * \return true - file written successfully, false - writing failed
|
---|
478 | */
|
---|
479 | bool MoleculeListClass::StoreForcesFile(std::string &path, int *SortIndex)
|
---|
480 | {
|
---|
481 | bool status = true;
|
---|
482 | string filename(path);
|
---|
483 | filename += FORCESFILE;
|
---|
484 | ofstream ForcesFile(filename.c_str());
|
---|
485 | periodentafel *periode=World::getInstance().getPeriode();
|
---|
486 |
|
---|
487 | // open file for the force factors
|
---|
488 | LOG(1, "Saving force factors ... ");
|
---|
489 | if (!ForcesFile.fail()) {
|
---|
490 | //output << prefix << "Forces" << endl;
|
---|
491 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
|
---|
492 | periodentafel::const_iterator elemIter;
|
---|
493 | for(elemIter=periode->begin();elemIter!=periode->end();++elemIter){
|
---|
494 | if ((*ListRunner)->hasElement((*elemIter).first)) { // if this element got atoms
|
---|
495 | for(molecule::iterator atomIter = (*ListRunner)->begin(); atomIter !=(*ListRunner)->end();++atomIter){
|
---|
496 | if ((*atomIter)->getType()->getNumber() == (*elemIter).first) {
|
---|
497 | if (((*atomIter)->GetTrueFather() != NULL) && ((*atomIter)->GetTrueFather() != (*atomIter))) {// if there is a rea
|
---|
498 | ForcesFile << SortIndex[(*atomIter)->GetTrueFather()->getNr()] << "\t";
|
---|
499 | } else
|
---|
500 | // otherwise a -1 to indicate an added saturation hydrogen
|
---|
501 | ForcesFile << "-1\t";
|
---|
502 | }
|
---|
503 | }
|
---|
504 | }
|
---|
505 | }
|
---|
506 | ForcesFile << endl;
|
---|
507 | }
|
---|
508 | ForcesFile.close();
|
---|
509 | LOG(1, "done.");
|
---|
510 | } else {
|
---|
511 | status = false;
|
---|
512 | LOG(1, "failed to open file " << filename << ".");
|
---|
513 | }
|
---|
514 | ForcesFile.close();
|
---|
515 |
|
---|
516 | return status;
|
---|
517 | };
|
---|
518 |
|
---|
519 | /** Writes a config file for each molecule in the given \a **FragmentList.
|
---|
520 | * \param *out output stream for debugging
|
---|
521 | * \param &prefix path and prefix to the fragment config files
|
---|
522 | * \param *SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
|
---|
523 | * \param type desired type to store
|
---|
524 | * \return true - success (each file was written), false - something went wrong.
|
---|
525 | */
|
---|
526 | bool MoleculeListClass::OutputConfigForListOfFragments(std::string &prefix, int *SortIndex, ParserTypes type)
|
---|
527 | {
|
---|
528 | ofstream outputFragment;
|
---|
529 | std::string FragmentName;
|
---|
530 | bool result = true;
|
---|
531 | bool intermediateResult = true;
|
---|
532 | Vector BoxDimension;
|
---|
533 | char *FragmentNumber = NULL;
|
---|
534 | int FragmentCounter = 0;
|
---|
535 | ofstream output;
|
---|
536 | RealSpaceMatrix cell_size = World::getInstance().getDomain().getM();
|
---|
537 | RealSpaceMatrix cell_size_backup = cell_size;
|
---|
538 | int count=0;
|
---|
539 |
|
---|
540 | // store the fragments as config and as xyz
|
---|
541 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
|
---|
542 | // correct periodic
|
---|
543 | if ((*ListRunner)->ScanForPeriodicCorrection()) {
|
---|
544 | count++;
|
---|
545 | }
|
---|
546 |
|
---|
547 | {
|
---|
548 | // list atoms in fragment for debugging
|
---|
549 | std::stringstream output;
|
---|
550 | output << "Contained atoms: ";
|
---|
551 | for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
|
---|
552 | output << (*iter)->getName() << " ";
|
---|
553 | }
|
---|
554 | LOG(2, output.str());
|
---|
555 | }
|
---|
556 |
|
---|
557 | {
|
---|
558 | // center on edge
|
---|
559 | (*ListRunner)->CenterEdge(&BoxDimension);
|
---|
560 | for (int k = 0; k < NDIM; k++) // if one edge is to small, set at least to 1 angstroem
|
---|
561 | if (BoxDimension[k] < 1.)
|
---|
562 | BoxDimension[k] += 1.;
|
---|
563 | (*ListRunner)->SetBoxDimension(&BoxDimension); // update Box of atoms by boundary
|
---|
564 | for (int k = 0; k < NDIM; k++) {
|
---|
565 | BoxDimension[k] = 2.5 * (World::getInstance().getConfig()->GetIsAngstroem() ? 1. : 1. / AtomicLengthToAngstroem);
|
---|
566 | cell_size.at(k,k) = BoxDimension[k] * 2.;
|
---|
567 | }
|
---|
568 | World::getInstance().setDomain(cell_size);
|
---|
569 | (*ListRunner)->Translate(&BoxDimension);
|
---|
570 |
|
---|
571 | // output file
|
---|
572 | std::vector<atom *> atoms;
|
---|
573 | // TODO: Convert iterator to const_iterator when FormatParserStorage::save() has vector<const atom *>
|
---|
574 | // We need iterator here because FormatParserStorage::save() need vector<atom *> not const refs.
|
---|
575 | for (molecule::iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter) {
|
---|
576 | atoms.push_back(*iter);
|
---|
577 | }
|
---|
578 | FragmentNumber = FixedDigitNumber(ListOfMolecules.size(), FragmentCounter++);
|
---|
579 | FragmentName = prefix + FragmentNumber + "." + FormatParserStorage::getInstance().getSuffixFromType(type);
|
---|
580 | outputFragment.open(FragmentName.c_str(), ios::out);
|
---|
581 | std::stringstream output;
|
---|
582 | output << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ... ";
|
---|
583 | if ((intermediateResult = FormatParserStorage::getInstance().save(
|
---|
584 | outputFragment,
|
---|
585 | FormatParserStorage::getInstance().getSuffixFromType(type),
|
---|
586 | atoms)))
|
---|
587 | output << " done.";
|
---|
588 | else
|
---|
589 | output << " failed.";
|
---|
590 | LOG(3, output.str());
|
---|
591 | delete[](FragmentNumber);
|
---|
592 |
|
---|
593 | result = result && intermediateResult;
|
---|
594 | outputFragment.close();
|
---|
595 | outputFragment.clear();
|
---|
596 | }
|
---|
597 | }
|
---|
598 | LOG(0, "STATUS: done.");
|
---|
599 |
|
---|
600 | // printing final number
|
---|
601 | LOG(2, "INFO: Final number of fragments: " << FragmentCounter << ".");
|
---|
602 |
|
---|
603 | // printing final number
|
---|
604 | LOG(2, "INFO: For " << count << " fragments periodic correction would have been necessary.");
|
---|
605 |
|
---|
606 | // restore cell_size
|
---|
607 | World::getInstance().setDomain(cell_size_backup);
|
---|
608 |
|
---|
609 | return result;
|
---|
610 | };
|
---|
611 |
|
---|
612 | /** Counts the number of molecules with the molecule::ActiveFlag set.
|
---|
613 | * \return number of molecules with ActiveFlag set to true.
|
---|
614 | */
|
---|
615 | int MoleculeListClass::NumberOfActiveMolecules()
|
---|
616 | {
|
---|
617 | int count = 0;
|
---|
618 | for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
|
---|
619 | count += ((*ListRunner)->ActiveFlag ? 1 : 0);
|
---|
620 | return count;
|
---|
621 | };
|
---|
622 |
|
---|
623 | /** Count all atoms in each molecule.
|
---|
624 | * \return number of atoms in the MoleculeListClass.
|
---|
625 | * TODO: the inner loop should be done by some (double molecule::CountAtom()) function
|
---|
626 | */
|
---|
627 | int MoleculeListClass::CountAllAtoms() const
|
---|
628 | {
|
---|
629 | int AtomNo = 0;
|
---|
630 | for (MoleculeList::const_iterator MolWalker = ListOfMolecules.begin(); MolWalker != ListOfMolecules.end(); MolWalker++) {
|
---|
631 | AtomNo += (*MolWalker)->size();
|
---|
632 | }
|
---|
633 | return AtomNo;
|
---|
634 | }
|
---|