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) 2012 University of Bonn. All rights reserved.
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5 | * Copyright (C) 2013 Frederik Heber. All rights reserved.
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6 | *
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7 | *
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8 | * This file is part of MoleCuilder.
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9 | *
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10 | * MoleCuilder is free software: you can redistribute it and/or modify
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11 | * it under the terms of the GNU General Public License as published by
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12 | * the Free Software Foundation, either version 2 of the License, or
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13 | * (at your option) any later version.
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14 | *
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15 | * MoleCuilder is distributed in the hope that it will be useful,
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16 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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17 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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18 | * GNU General Public License for more details.
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19 | *
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20 | * You should have received a copy of the GNU General Public License
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21 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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22 | */
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23 |
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24 | /*
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25 | * AnalyseFragmentationResultsAction.cpp
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26 | *
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27 | * Created on: Mar 8, 2013
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28 | * Author: heber
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29 | */
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30 |
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31 | // include config.h
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32 | #ifdef HAVE_CONFIG_H
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33 | #include <config.h>
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34 | #endif
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35 |
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36 | // include headers that implement a archive in simple text format
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37 | // and before MemDebug due to placement new
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38 | #include <boost/archive/text_oarchive.hpp>
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39 | #include <boost/archive/text_iarchive.hpp>
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40 |
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41 | //#include "CodePatterns/MemDebug.hpp"
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42 |
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43 | #include <boost/foreach.hpp>
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44 | #include <boost/lambda/lambda.hpp>
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45 | #include <boost/mpl/remove.hpp>
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46 |
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47 | #include <algorithm>
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48 | #include <fstream>
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49 | #include <iostream>
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50 | //#include <numeric>
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51 | #include <string>
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52 | #include <vector>
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53 |
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54 | #include "CodePatterns/Assert.hpp"
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55 | #include "CodePatterns/Log.hpp"
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56 |
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57 | #ifdef HAVE_JOBMARKET
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58 | #include "JobMarket/types.hpp"
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59 | #else
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60 | typedef size_t JobId_t;
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61 | #endif
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62 |
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63 | #include "Descriptors/AtomIdDescriptor.hpp"
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64 | #include "Atom/atom.hpp"
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65 | #include "Element/element.hpp"
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66 | #include "Fragmentation/EdgesPerFragment.hpp"
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67 | #include "Fragmentation/Exporters/ExportGraph_ToJobs.hpp"
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68 | #include "Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp"
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69 | #include "Fragmentation/Summation/Containers/FragmentationResultContainer.hpp"
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70 | #include "Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp"
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71 | #include "Fragmentation/Summation/Containers/MPQCData.hpp"
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72 | #include "Fragmentation/Summation/Containers/MPQCData_printKeyNames.hpp"
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73 | #include "Fragmentation/Homology/HomologyContainer.hpp"
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74 | #include "Fragmentation/Homology/HomologyGraph.hpp"
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75 | #include "Fragmentation/KeySetsContainer.hpp"
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76 | #include "Fragmentation/Summation/SetValues/Eigenvalues.hpp"
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77 | #include "Fragmentation/Summation/SetValues/Fragment.hpp"
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78 | #include "Fragmentation/Summation/SetValues/FragmentForces.hpp"
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79 | #include "Fragmentation/Summation/SetValues/Histogram.hpp"
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80 | #include "Fragmentation/Summation/SetValues/IndexedVectors.hpp"
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81 | #include "Fragmentation/Summation/IndexSetContainer.hpp"
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82 | #include "Fragmentation/Summation/writeIndexedTable.hpp"
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83 | #include "Fragmentation/Summation/writeTable.hpp"
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84 | #if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
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85 | #include "Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp"
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86 | #include "Fragmentation/Summation/Containers/GridDownsampler.hpp"
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87 | #include "Fragmentation/Summation/Containers/VMGData.hpp"
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88 | #include "Fragmentation/Summation/Containers/VMGDataFused.hpp"
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89 | #include "Fragmentation/Summation/Containers/VMGDataMap.hpp"
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90 | #include "Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp"
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91 | #endif
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92 | #include "Helpers/defs.hpp"
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93 | #include "Potentials/Particles/ParticleRegistry.hpp"
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94 | #include "World.hpp"
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95 |
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96 | #include "Actions/FragmentationAction/AnalyseFragmentationResultsAction.hpp"
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97 |
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98 | using namespace MoleCuilder;
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99 |
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100 | // and construct the stuff
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101 | #include "AnalyseFragmentationResultsAction.def"
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102 | #include "Action_impl_pre.hpp"
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103 | /** =========== define the function ====================== */
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104 |
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105 | void writeToFile(const std::string &filename, const std::string contents)
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106 | {
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107 | std::ofstream tablefile(filename.c_str());
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108 | tablefile << contents;
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109 | tablefile.close();
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110 | }
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111 |
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112 | /** Print cycle correction from received results.
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113 | *
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114 | * @param results summed up results container
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115 | */
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116 | void printReceivedCycleResults(
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117 | const FragmentationShortRangeResults &results)
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118 | {
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119 | typedef boost::mpl::remove<
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120 | boost::mpl::remove<MPQCDataEnergyVector_t, MPQCDataFused::energy_eigenvalues>::type,
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121 | MPQCDataFused::energy_eigenhistogram>::type
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122 | MPQCDataEnergyVector_noeigenvalues_t;
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123 | const std::string energyresult =
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124 | writeTable<MPQCDataEnergyMap_t, MPQCDataEnergyVector_noeigenvalues_t >()(
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125 | results.Result_Energy_fused, results.getMaxLevel());
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126 | LOG(2, "DEBUG: Energy table is \n" << energyresult);
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127 | std::string filename;
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128 | filename += FRAGMENTPREFIX + std::string("_CycleEnergy.dat");
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129 | writeToFile(filename, energyresult);
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130 | }
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131 |
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132 | /** Print (short range) energy, forces, and timings from received results per index set.
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133 | *
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134 | * @param results summed up results container
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135 | */
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136 | void printReceivedShortResultsPerIndex(
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137 | const FragmentationShortRangeResults &results)
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138 | {
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139 | // print tables per keyset(without eigenvalues, they go extra)
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140 | typedef boost::mpl::remove<
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141 | boost::mpl::remove<MPQCDataEnergyVector_t, MPQCDataFused::energy_eigenvalues>::type,
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142 | MPQCDataFused::energy_eigenhistogram>::type
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143 | MPQCDataEnergyVector_noeigenvalues_t;
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144 | const std::string energyresult =
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145 | writeIndexedTable<MPQCDataEnergyMap_t, MPQCDataEnergyVector_noeigenvalues_t >()(
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146 | results.Result_perIndexSet_Energy, results.getMaxLevel());
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147 | LOG(2, "DEBUG: Indexed Energy table is \n" << energyresult);
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148 | std::string filename;
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149 | filename += FRAGMENTPREFIX + std::string("_IndexedEnergy.dat");
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150 | writeToFile(filename, energyresult);
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151 | }
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152 |
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153 | /** Print (short range) energy, forces, and timings from received results.
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154 | *
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155 | * @param results summed up results container
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156 | */
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157 | void printReceivedShortResults(
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158 | const FragmentationShortRangeResults &results)
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159 | {
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160 | // print tables (without eigenvalues, they go extra)
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161 | {
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162 | typedef boost::mpl::remove<
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163 | boost::mpl::remove<MPQCDataEnergyVector_t, MPQCDataFused::energy_eigenvalues>::type,
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164 | MPQCDataFused::energy_eigenhistogram>::type
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165 | MPQCDataEnergyVector_noeigenvalues_t;
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166 | const std::string energyresult =
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167 | writeTable<MPQCDataEnergyMap_t, MPQCDataEnergyVector_noeigenvalues_t >()(
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168 | results.Result_Energy_fused, results.getMaxLevel());
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169 | LOG(2, "DEBUG: Energy table is \n" << energyresult);
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170 | std::string filename;
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171 | filename += FRAGMENTPREFIX + std::string("_Energy.dat");
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172 | writeToFile(filename, energyresult);
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173 | }
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174 |
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175 | {
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176 | typedef boost::mpl::list<
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177 | MPQCDataFused::energy_eigenvalues
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178 | > MPQCDataEigenvalues_t;
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179 | const std::string eigenvalueresult =
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180 | writeTable<MPQCDataEnergyMap_t, MPQCDataEigenvalues_t >()(
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181 | results.Result_Energy_fused, results.getMaxLevel());
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182 | LOG(2, "DEBUG: Eigenvalue table is \n" << eigenvalueresult);
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183 | std::string filename;
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184 | filename += FRAGMENTPREFIX + std::string("_Eigenvalues.dat");
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185 | writeToFile(filename, eigenvalueresult);
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186 | }
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187 |
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188 | {
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189 | typedef boost::mpl::list<
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190 | MPQCDataFused::energy_eigenhistogram
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191 | > MPQCDataEigenhistogram_t;
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192 | const std::string eigenhistogramresult =
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193 | writeTable<MPQCDataEnergyMap_t, MPQCDataEigenhistogram_t >()(
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194 | results.Result_Energy_fused, results.getMaxLevel());
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195 | LOG(2, "DEBUG: Eigenhistogram table is \n" << eigenhistogramresult);
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196 | std::string filename;
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197 | filename += FRAGMENTPREFIX + std::string("_Eigenhistogram.dat");
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198 | writeToFile(filename, eigenhistogramresult);
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199 | }
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200 |
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201 | {
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202 | typedef boost::mpl::list<
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203 | MPQCDataFused::energy_eigenvalues
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204 | > MPQCDataEigenvalues_t;
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205 | const std::string eigenvalueresult =
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206 | writeTable<MPQCDataEnergyMap_t, MPQCDataEigenvalues_t >()(
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207 | results.Result_Energy_fused, results.getMaxLevel());
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208 | LOG(2, "DEBUG: Eigenvalue table is \n" << eigenvalueresult);
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209 | std::string filename;
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210 | filename += FRAGMENTPREFIX + std::string("_Eigenvalues.dat");
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211 | writeToFile(filename, eigenvalueresult);
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212 | }
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213 |
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214 | {
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215 | const std::string forceresult =
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216 | writeTable<MPQCDataForceMap_t, MPQCDataForceVector_t>()(
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217 | results.Result_Force_fused, results.getMaxLevel());
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218 | LOG(2, "DEBUG: Force table is \n" << forceresult);
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219 | std::string filename;
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220 | filename += FRAGMENTPREFIX + std::string("_Forces.dat");
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221 | writeToFile(filename, forceresult);
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222 | }
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223 | // we don't want to print grid to a table
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224 | {
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225 | // print times (without flops for now)
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226 | typedef boost::mpl::remove<
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227 | boost::mpl::remove<MPQCDataTimeVector_t, MPQCDataFused::times_total_flops>::type,
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228 | MPQCDataFused::times_gather_flops>::type
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229 | MPQCDataTimeVector_noflops_t;
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230 | const std::string timesresult =
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231 | writeTable<MPQCDataTimeMap_t, MPQCDataTimeVector_noflops_t >()(
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232 | results.Result_Time_fused, results.getMaxLevel());
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233 | LOG(2, "DEBUG: Times table is \n" << timesresult);
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234 | std::string filename;
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235 | filename += FRAGMENTPREFIX + std::string("_Times.dat");
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236 | writeToFile(filename, timesresult);
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237 | }
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238 | }
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239 |
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240 |
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241 | #if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
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242 | /** Print long range energy from received results.
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243 | *
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244 | * @param results summed up results container
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245 | */
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246 | void printReceivedFullResults(
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247 | const FragmentationLongRangeResults &results)
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248 | {
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249 | // print tables per keyset(without grids, they go extra)
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250 |
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251 | {
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252 | const std::string gridresult =
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253 | writeTable<VMGDataMap_t, VMGDataVector_t >()(
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254 | results.Result_LongRange_fused, results.getMaxLevel(), 1);
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255 | LOG(2, "DEBUG: VMG table is \n" << gridresult);
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256 | std::string filename;
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257 | filename += FRAGMENTPREFIX + std::string("_VMGEnergy.dat");
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258 | writeToFile(filename, gridresult);
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259 | }
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260 |
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261 | if (results.hasLongRangeForces()) {
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262 | const std::string forceresult =
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263 | writeTable<VMGDataForceMap_t, VMGDataForceVector_t>()(
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264 | results.Result_ForceLongRange_fused, results.getMaxLevel());
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265 | LOG(2, "DEBUG: Force table is \n" << forceresult);
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266 | std::string filename;
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267 | filename += FRAGMENTPREFIX + std::string("_VMGForces.dat");
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268 | writeToFile(filename, forceresult);
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269 | }
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270 |
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271 | {
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272 | const std::string gridresult =
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273 | writeTable<VMGDataLongRangeMap_t, VMGDataLongRangeVector_t >()(
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274 | results.Result_LongRangeIntegrated_fused, results.getMaxLevel(), 1);
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275 | LOG(2, "DEBUG: LongRange table is \n" << gridresult);
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276 | std::string filename;
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277 | filename += FRAGMENTPREFIX + std::string("_LongRangeEnergy.dat");
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278 | writeToFile(filename, gridresult);
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279 | }
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280 |
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281 | if (results.hasLongRangeForces()) {
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282 | const std::string forceresult =
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283 | writeTable<VMGDataLongRangeForceMap_t, VMGDataLongRangeForceVector_t >()(
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284 | results.Result_ForcesLongRangeIntegrated_fused, results.getMaxLevel(), 1);
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285 | LOG(2, "DEBUG: ForcesLongRange table is \n" << forceresult);
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286 | std::string filename;
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287 | filename += FRAGMENTPREFIX + std::string("_LongRangeForces.dat");
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288 | writeToFile(filename, forceresult);
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289 | }
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290 | }
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291 | #endif
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292 |
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293 | bool appendToHomologies(
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294 | const FragmentationShortRangeResults &shortrangeresults,
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295 | #if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
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296 | const FragmentationLongRangeResults &longrangeresults,
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297 | #endif
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298 | const bool storeGrids
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299 | )
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300 | {
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301 | /// read homology container (if present)
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302 | HomologyContainer &homology_container = World::getInstance().getHomologies();
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303 |
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304 | /// append all fragments to a HomologyContainer
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305 | HomologyContainer::container_t values;
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306 |
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307 | // convert KeySetContainer to IndexSetContainer
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308 | // BUG: Conversion changes order w.r.t to Indices(!)
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309 | const IndexSetContainer::Container_t &container = shortrangeresults.getContainer();
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310 | const KeySetsContainer &Indices = shortrangeresults.getKeySet();
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311 | const KeySetsContainer &ForceIndices = shortrangeresults.getForceKeySet();
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312 | const FragmentationEdges::edges_per_fragment_t &edges_per_fragment =
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313 | shortrangeresults.getEdgesPerFragment();
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314 | if (Indices.KeySets.size() != ForceIndices.KeySets.size()) {
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315 | ELOG(1, "appendToHomologies() - Indices (" << Indices.KeySets.size()
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316 | << ") and ForceIndices (" << ForceIndices.KeySets.size() << ") sizes differ.");
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317 | return false;
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318 | }
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319 | if (Indices.KeySets.size() != edges_per_fragment.size()) {
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320 | ELOG(1, "appendToHomologies() - Indices (" << Indices.KeySets.size()
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321 | << ") and edges_per_fragment (" << edges_per_fragment.size() << ") sizes differ.");
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322 | return false;
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323 | }
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324 | KeySetsContainer::ArrayOfIntVectors::const_iterator iter = Indices.KeySets.begin();
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325 | KeySetsContainer::ArrayOfIntVectors::const_iterator forceiter = ForceIndices.KeySets.begin();
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326 | FragmentationEdges::edges_per_fragment_t::const_iterator edgeiter = edges_per_fragment.begin();
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327 |
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328 | /// go through all fragments
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329 | for (;iter != Indices.KeySets.end(); ++iter, ++forceiter, ++edgeiter) // go through each IndexSet
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330 | {
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331 | /// create new graph entry in HomologyContainer which is (key,value) type
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332 | LOG(1, "INFO: Creating new graph with " << *forceiter << ".");
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333 | IndexSet forceindexset;
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334 | forceindexset.insert(forceiter->begin(), forceiter->end());
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335 | const HomologyGraph graph(forceindexset);
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336 | // get index set entity from container for lookup to fragment result
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337 | IndexSet::ptr indexset(new IndexSet);
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338 | indexset->insert(iter->begin(), iter->end());
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339 | if (!forceindexset.contains(*indexset)) {
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340 | // this caught an error with faulty KeySetsContainer::insert().
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341 | // indexset and forceindexset need to be in same order and differ
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342 | // only in forceindexset contains extra indices for saturation hydrogens
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343 | ELOG(1, "appendToHomologies() - force index set " << forceindexset
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344 | << " does not contain index set " << (*indexset) << ".");
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345 | return false;
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346 | }
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347 | const IndexSetContainer::Container_t::const_iterator indexiter =
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348 | std::lower_bound(container.begin(), container.end(), indexset);
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349 | const IndexSet::ptr &index = *indexiter;
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350 | ASSERT( *index == *indexset,
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351 | "appendToHomologies() - could not find index set "+toString(*indexset)
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352 | +" in the sorted IndexSetContainer.");
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353 |
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354 |
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355 | /// we fill the value structure
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356 | HomologyContainer::value_t value;
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357 | value.containsGrids = storeGrids;
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358 | // obtain fragment
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359 | std::map<IndexSet::ptr, std::pair< MPQCDataFragmentMap_t, MPQCDataFragmentMap_t> >::const_iterator fragmentiter
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360 | = shortrangeresults.Result_perIndexSet_Fragment.find(index);
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361 | if (fragmentiter == shortrangeresults.Result_perIndexSet_Fragment.end()) {
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362 | ELOG(1, "appendToHomologyFile() - cannot find index " << (*index)
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363 | << " in FragmentResults.");
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364 | return false;
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365 | }
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366 | value.fragment = boost::fusion::at_key<MPQCDataFused::fragment>(fragmentiter->second.first);
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367 | LOG(1, "DEBUG: Created graph " << graph << " to fragment " << value.fragment << ".");
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368 |
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369 | // obtain energy
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370 | std::map<IndexSet::ptr, std::pair< MPQCDataEnergyMap_t, MPQCDataEnergyMap_t> >::const_iterator energyiter
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371 | = shortrangeresults.Result_perIndexSet_Energy.find(index);
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372 | if (energyiter == shortrangeresults.Result_perIndexSet_Energy.end()) {
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373 | ELOG(1, "appendToHomologyFile() - cannot find index " << (*index)
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374 | << " in FragmentResults.");
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375 | return false;
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376 | }
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377 | value.edges = *edgeiter;
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378 | value.energy = boost::fusion::at_key<MPQCDataFused::energy_total>(energyiter->second.second); // contributions
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379 |
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380 | // only store sampled grids if desired
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381 | if (storeGrids) {
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382 | #if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
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383 | // obtain charge distribution
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384 | std::map<IndexSet::ptr, std::pair< MPQCDataGridMap_t, MPQCDataGridMap_t> >::const_iterator chargeiter
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385 | = longrangeresults.Result_perIndexSet_Grid.find(index);
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386 | if (chargeiter == longrangeresults.Result_perIndexSet_Grid.end()) {
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387 | ELOG(1, "appendToHomologyFile() - cannot find index " << (*index)
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388 | << " in FragmentResults.");
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389 | return false;
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390 | }
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391 | value.charge_distribution = boost::fusion::at_key<MPQCDataFused::sampled_grid>(chargeiter->second.second); // contributions
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392 |
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393 | // obtain potential distribution
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394 | std::map<IndexSet::ptr, std::pair< VMGDataGridMap_t, VMGDataGridMap_t> >::const_iterator potentialiter
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395 | = longrangeresults.Result_perIndexSet_LongRange_Grid.find(index);
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396 | if (potentialiter == longrangeresults.Result_perIndexSet_LongRange_Grid.end()) {
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397 | ELOG(1, "appendToHomologyFile() - cannot find index " << (*index)
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398 | << " in FragmentResults.");
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399 | return false;
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400 | }
|
---|
401 | // add e+n potentials
|
---|
402 | value.potential_distribution =
|
---|
403 | boost::fusion::at_key<VMGDataFused::both_sampled_potential>(potentialiter->second.second); // contributions
|
---|
404 | // // and re-average to zero (integral is times volume_element which we don't need here)
|
---|
405 | // const double sum =
|
---|
406 | // std::accumulate(
|
---|
407 | // value.potential_distribution.sampled_grid.begin(),
|
---|
408 | // value.potential_distribution.sampled_grid.end(),
|
---|
409 | // 0.);
|
---|
410 | // const double offset = sum/(double)value.potential_distribution.sampled_grid.size();
|
---|
411 | // for (SamplingGrid::sampledvalues_t::iterator iter = value.potential_distribution.sampled_grid.begin();
|
---|
412 | // iter != value.potential_distribution.sampled_grid.end();
|
---|
413 | // ++iter)
|
---|
414 | // *iter -= offset;
|
---|
415 | #else
|
---|
416 | ELOG(2, "Long-range information in homology desired but long-range analysis capability not compiled in.");
|
---|
417 | #endif
|
---|
418 | }
|
---|
419 | values.insert( std::make_pair( graph, value) );
|
---|
420 | }
|
---|
421 | homology_container.insert(values);
|
---|
422 |
|
---|
423 | if (DoLog(2)) {
|
---|
424 | LOG(2, "DEBUG: Listing all present atomic ids ...");
|
---|
425 | std::stringstream output;
|
---|
426 | for (World::AtomIterator iter = World::getInstance().getAtomIter();
|
---|
427 | iter != World::getInstance().atomEnd(); ++iter)
|
---|
428 | output << (*iter)->getId() << " ";
|
---|
429 | LOG(2, "DEBUG: { " << output.str() << "} .");
|
---|
430 | }
|
---|
431 |
|
---|
432 | // for debugging: print container
|
---|
433 | if (DoLog(2)) {
|
---|
434 | LOG(2, "DEBUG: Listing all present homologies ...");
|
---|
435 | for (HomologyContainer::container_t::const_iterator iter =
|
---|
436 | homology_container.begin(); iter != homology_container.end(); ++iter) {
|
---|
437 | std::stringstream output;
|
---|
438 | output << "DEBUG: graph " << iter->first
|
---|
439 | << " has Fragment " << iter->second.fragment
|
---|
440 | << ", associated energy " << iter->second.energy;
|
---|
441 | if (iter->second.containsGrids)
|
---|
442 | #if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
|
---|
443 | output << ", and sampled grid integral " << iter->second.charge_distribution.integral();
|
---|
444 | #else
|
---|
445 | output << ", and there are sampled grids but capability not compiled in";
|
---|
446 | #endif
|
---|
447 | output << ".";
|
---|
448 | LOG(2, output.str());
|
---|
449 | }
|
---|
450 | }
|
---|
451 |
|
---|
452 | return true;
|
---|
453 | }
|
---|
454 |
|
---|
455 | // this it taken from
|
---|
456 | // http://stackoverflow.com/questions/2291802/is-there-a-c-iterator-that-can-iterate-over-a-file-line-by-line
|
---|
457 | namespace detail
|
---|
458 | {
|
---|
459 | /** Extend the string class by a friend function.
|
---|
460 | *
|
---|
461 | */
|
---|
462 | class Line : public std::string
|
---|
463 | {
|
---|
464 | friend std::istream & operator>>(std::istream & is, Line & line)
|
---|
465 | {
|
---|
466 | return std::getline(is, line);
|
---|
467 | }
|
---|
468 | };
|
---|
469 | }
|
---|
470 |
|
---|
471 | /** Parse the given stream line-by-line, passing each to \a dest.
|
---|
472 | *
|
---|
473 | * \param is stream to parse line-wise
|
---|
474 | * \param dest output iterator
|
---|
475 | */
|
---|
476 | template<class OutIt>
|
---|
477 | void read_lines(std::istream& is, OutIt dest)
|
---|
478 | {
|
---|
479 | typedef std::istream_iterator<detail::Line> InIt;
|
---|
480 | std::copy(InIt(is), InIt(), dest);
|
---|
481 | }
|
---|
482 |
|
---|
483 |
|
---|
484 | /** Determines the largest cycle in the container and returns its size.
|
---|
485 | *
|
---|
486 | * \param cycles set of cycles
|
---|
487 | * \return size if largest cycle
|
---|
488 | */
|
---|
489 | size_t getMaxCycleSize(const KeySetsContainer &cycles)
|
---|
490 | {
|
---|
491 | // gather cycle sizes
|
---|
492 | std::vector<size_t> cyclesizes(cycles.KeySets.size());
|
---|
493 | std::transform(
|
---|
494 | cycles.KeySets.begin(), cycles.KeySets.end(),
|
---|
495 | cyclesizes.begin(),
|
---|
496 | boost::bind(&KeySetsContainer::IntVector::size, boost::lambda::_1)
|
---|
497 | );
|
---|
498 | // get maximum
|
---|
499 | std::vector<size_t>::const_iterator maximum_size =
|
---|
500 | std::max_element(cyclesizes.begin(), cyclesizes.end());
|
---|
501 | if (maximum_size != cyclesizes.end())
|
---|
502 | return *maximum_size;
|
---|
503 | else
|
---|
504 | return 0;
|
---|
505 | }
|
---|
506 |
|
---|
507 | void calculateCycleFullContribution(
|
---|
508 | const std::map<JobId_t, MPQCData> &shortrangedata,
|
---|
509 | const KeySetsContainer &keysets,
|
---|
510 | const KeySetsContainer &forcekeysets,
|
---|
511 | const KeySetsContainer &cycles,
|
---|
512 | const FragmentationShortRangeResults::edges_per_fragment_t &edges_per_fragment,
|
---|
513 | const FragmentationShortRangeResults &shortrangeresults)
|
---|
514 | {
|
---|
515 | // copy the shortrangeresults such that private MaxLevel is set in
|
---|
516 | // FragmentationShortRangeResults
|
---|
517 | FragmentationShortRangeResults cycleresults(shortrangeresults);
|
---|
518 | // get largest size
|
---|
519 | const size_t maximum_size = getMaxCycleSize(cycles);
|
---|
520 |
|
---|
521 | /// The idea here is that (Orthogonal)Summation will place a result
|
---|
522 | /// consisting of level 1,2, and 3 fragment and a level 6 ring nonetheless
|
---|
523 | /// in level 6. If we want to have this result already at level 3, we
|
---|
524 | /// have to specifically inhibit all fragments from later levels but the
|
---|
525 | /// cycles and then pick the result from the last level and placing it at
|
---|
526 | /// the desired one
|
---|
527 |
|
---|
528 | // loop from level 1 to max ring size and gather contributions
|
---|
529 | for (size_t level = 1; level <= maximum_size; ++level) {
|
---|
530 | // create ValueMask for this level by stepping through each keyset and checking size
|
---|
531 | std::vector<bool> localValueMask(shortrangedata.size(), false);
|
---|
532 | size_t index=0;
|
---|
533 | // TODO: if only KeySetsContainer was usable as a compliant STL container, might be able to use set_difference or alike.
|
---|
534 | KeySetsContainer::ArrayOfIntVectors::const_iterator keysetsiter = keysets.KeySets.begin();
|
---|
535 | KeySetsContainer::ArrayOfIntVectors::const_iterator cyclesiter = cycles.KeySets.begin();
|
---|
536 | for (; (keysetsiter != keysets.KeySets.end()) && (cyclesiter != cycles.KeySets.end());) {
|
---|
537 | if (cyclesiter->size() > keysetsiter->size()) {
|
---|
538 | // add if not greater than level in size
|
---|
539 | if ((*keysetsiter).size() <= level)
|
---|
540 | localValueMask[index] = true;
|
---|
541 | ++keysetsiter;
|
---|
542 | ++index;
|
---|
543 | } else if (cyclesiter->size() < keysetsiter->size()) {
|
---|
544 | ++cyclesiter;
|
---|
545 | } else { // both sets have same size
|
---|
546 | if (*cyclesiter > *keysetsiter) {
|
---|
547 | // add if not greater than level in size
|
---|
548 | if ((*keysetsiter).size() <= level)
|
---|
549 | localValueMask[index] = true;
|
---|
550 | ++keysetsiter;
|
---|
551 | ++index;
|
---|
552 | } else if (*cyclesiter < *keysetsiter) {
|
---|
553 | ++cyclesiter;
|
---|
554 | } else {
|
---|
555 | // also always add all cycles
|
---|
556 | localValueMask[index] = true;
|
---|
557 | ++cyclesiter;
|
---|
558 | ++keysetsiter;
|
---|
559 | ++index;
|
---|
560 | }
|
---|
561 | }
|
---|
562 | }
|
---|
563 | // activate rest if desired by level
|
---|
564 | for (; keysetsiter != keysets.KeySets.end(); ++keysetsiter) {
|
---|
565 | if ((*keysetsiter).size() <= level)
|
---|
566 | localValueMask[index] = true;
|
---|
567 | ++index;
|
---|
568 | }
|
---|
569 | LOG(2, "DEBUG: ValueMask for cycle correction at level " << level << " is "
|
---|
570 | << localValueMask << ".");
|
---|
571 | // create FragmentationShortRangeResults
|
---|
572 | FragmentationShortRangeResults localresults(
|
---|
573 | shortrangedata, keysets, forcekeysets, edges_per_fragment, localValueMask);
|
---|
574 | // and perform summation
|
---|
575 | localresults(shortrangedata);
|
---|
576 | // finally, extract the corrections from last level
|
---|
577 | cycleresults.Result_Energy_fused[level-1] =
|
---|
578 | localresults.Result_Energy_fused.back();
|
---|
579 | cycleresults.Result_Time_fused[level-1] =
|
---|
580 | localresults.Result_Time_fused.back();
|
---|
581 | cycleresults.Result_Force_fused[level-1] =
|
---|
582 | localresults.Result_Force_fused.back();
|
---|
583 | }
|
---|
584 | printReceivedCycleResults(cycleresults);
|
---|
585 | }
|
---|
586 |
|
---|
587 | static void AddForces(
|
---|
588 | const IndexedVectors::indexedvectors_t &_forces,
|
---|
589 | const bool _IsAngstroem)
|
---|
590 | {
|
---|
591 | for(IndexedVectors::indexedvectors_t::const_iterator iter = _forces.begin();
|
---|
592 | iter != _forces.end(); ++iter) {
|
---|
593 | const IndexedVectors::index_t &index = iter->first;
|
---|
594 | const IndexedVectors::vector_t &forcevector = iter->second;
|
---|
595 | ASSERT( forcevector.size() == NDIM,
|
---|
596 | "printReceivedShortResults() - obtained force vector has incorrect dimension.");
|
---|
597 | // note that mpqc calculates a gradient, hence force pointing into opposite direction
|
---|
598 | // we have to mind different units here: MPQC has a_o, while we may have angstroem
|
---|
599 | Vector ForceVector(-forcevector[0], -forcevector[1], -forcevector[2]);
|
---|
600 | if (_IsAngstroem)
|
---|
601 | for (size_t i=0;i<NDIM;++i)
|
---|
602 | ForceVector[i] *= AtomicLengthToAngstroem;
|
---|
603 | atom *_atom = World::getInstance().getAtom(AtomById(index));
|
---|
604 | if(_atom != NULL)
|
---|
605 | _atom->setAtomicForce(_atom->getAtomicForce() + ForceVector);
|
---|
606 | else
|
---|
607 | ELOG(2, "Could not find atom to id " << index << ".");
|
---|
608 | }
|
---|
609 | }
|
---|
610 |
|
---|
611 | ActionState::ptr FragmentationAnalyseFragmentationResultsAction::performCall() {
|
---|
612 | bool status=true;
|
---|
613 |
|
---|
614 | /// get data and keysets from ResultsContainer
|
---|
615 | FragmentationResultContainer& container = FragmentationResultContainer::getInstance();
|
---|
616 | const std::map<JobId_t, MPQCData> &shortrangedata = container.getShortRangeResults();
|
---|
617 | const KeySetsContainer &keysets = container.getKeySets();
|
---|
618 | const KeySetsContainer &forcekeysets = container.getForceKeySets();
|
---|
619 | const FragmentationResultContainer::edges_per_fragment_t edges_per_fragment =
|
---|
620 | container.getEdgesPerFragment();
|
---|
621 | const bool DoLongrange = container.areFullRangeResultsPresent();
|
---|
622 | const bool IsAngstroem = true;
|
---|
623 |
|
---|
624 | if (keysets.KeySets.empty()) {
|
---|
625 | STATUS("There are no results in the container.");
|
---|
626 | return Action::failure;
|
---|
627 | }
|
---|
628 |
|
---|
629 | /// calculate normal contributions with (if present) cycles coming at their
|
---|
630 | /// respective bond order.
|
---|
631 | std::vector<bool> ValueMask(shortrangedata.size(), true);
|
---|
632 | FragmentationShortRangeResults shortrangeresults(
|
---|
633 | shortrangedata, keysets, forcekeysets, edges_per_fragment, ValueMask);
|
---|
634 | shortrangeresults(shortrangedata);
|
---|
635 | printReceivedShortResults(shortrangeresults);
|
---|
636 | printReceivedShortResultsPerIndex(shortrangeresults);
|
---|
637 | // add summed results to container
|
---|
638 | container.addShortRangeSummedResults(shortrangeresults.getSummedShortRangeResults());
|
---|
639 |
|
---|
640 | /// now do we need to calculate the cycle contribution
|
---|
641 | // check whether there are cycles in container or else in file
|
---|
642 | KeySetsContainer cycles = container.getCycles();
|
---|
643 | if (cycles.KeySets.empty()) {
|
---|
644 | // parse from file if cycles is empty
|
---|
645 | boost::filesystem::path filename(
|
---|
646 | params.prefix.get() + std::string(CYCLEKEYSETFILE));
|
---|
647 | if (boost::filesystem::exists(filename)) {
|
---|
648 | LOG(1, "INFO: Parsing cycles file " << filename.string() << ".");
|
---|
649 | // parse file line by line
|
---|
650 | std::ifstream File;
|
---|
651 | File.open(filename.string().c_str());
|
---|
652 | typedef std::istream_iterator<detail::Line> InIt;
|
---|
653 | for (InIt iter = InIt(File); iter != InIt(); ++iter) {
|
---|
654 | KeySetsContainer::IntVector cycle;
|
---|
655 | std::stringstream line(*iter);
|
---|
656 | while (line.good()) {
|
---|
657 | int id;
|
---|
658 | line >> id >> ws;
|
---|
659 | cycle.push_back(id);
|
---|
660 | }
|
---|
661 | if (!cycle.empty()) {
|
---|
662 | LOG(2, "DEBUG: Adding cycle " << cycle << ".");
|
---|
663 | cycles.insert( cycle, cycle.size());
|
---|
664 | }
|
---|
665 | }
|
---|
666 | File.close();
|
---|
667 | } else {
|
---|
668 | LOG(1, "INFO: Cycles file not found at " << filename.string() << ".");
|
---|
669 | }
|
---|
670 | }
|
---|
671 |
|
---|
672 | // calculate energy if cycles are calculated fully at each level already
|
---|
673 | if (!cycles.KeySets.empty()) {
|
---|
674 | calculateCycleFullContribution(
|
---|
675 | shortrangedata,
|
---|
676 | keysets,
|
---|
677 | forcekeysets,
|
---|
678 | cycles,
|
---|
679 | edges_per_fragment,
|
---|
680 | shortrangeresults);
|
---|
681 | }
|
---|
682 |
|
---|
683 | // adding obtained forces
|
---|
684 | if ( const_cast<const World &>(World::getInstance()).getAllAtoms().size() != 0) {
|
---|
685 | const IndexedVectors::indexedvectors_t shortrange_forces =
|
---|
686 | boost::fusion::at_key<MPQCDataFused::forces>(
|
---|
687 | shortrangeresults.Result_Force_fused.back()
|
---|
688 | ).getVectors();
|
---|
689 | AddForces(shortrange_forces,IsAngstroem);
|
---|
690 | } else {
|
---|
691 | LOG(1, "INFO: Full molecule not loaded, hence will not add forces to atoms.");
|
---|
692 | }
|
---|
693 |
|
---|
694 | #if defined(HAVE_JOBMARKET) && defined(HAVE_VMG)
|
---|
695 | if (DoLongrange) {
|
---|
696 | if ( const_cast<const World &>(World::getInstance()).getAllAtoms().size() == 0) {
|
---|
697 | STATUS("Please load the full molecule into std::map<JobId_t, VMGData> longrangeData the world before starting this action.");
|
---|
698 | return Action::failure;
|
---|
699 | }
|
---|
700 |
|
---|
701 | std::map<JobId_t, VMGData> longrangeData = container.getLongRangeResults();
|
---|
702 |
|
---|
703 | ASSERT( !longrangeData.empty(),
|
---|
704 | "FragmentationAnalyseFragmentationResultsAction::performCall() - longrangeData is empty?");
|
---|
705 | // get required level from longrange full potential solution
|
---|
706 | const int level = longrangeData.rbegin()->second.sampled_potential.level;
|
---|
707 | SamplingGridProperties domain(ExportGraph_ToJobs::getDomainGrid(level));
|
---|
708 | SamplingGrid zero_globalgrid(domain);
|
---|
709 | FragmentationChargeDensity summedChargeDensity(shortrangedata);
|
---|
710 | summedChargeDensity(shortrangedata, keysets, zero_globalgrid);
|
---|
711 | const std::vector<SamplingGrid> full_sample = summedChargeDensity.getFullSampledGrid();
|
---|
712 |
|
---|
713 | // remove full solution corresponding to full_sample from map (must be highest ids), has to be treated extra
|
---|
714 | std::map<JobId_t, VMGData>::iterator iter = longrangeData.end();
|
---|
715 | std::advance(iter, -full_sample.size());
|
---|
716 | std::map<JobId_t, VMGData>::iterator remove_iter = iter;
|
---|
717 | std::vector<VMGData> fullsolutionData;
|
---|
718 | for (; iter != longrangeData.end(); ++iter)
|
---|
719 | fullsolutionData.push_back(iter->second);
|
---|
720 | if (longrangeData.size() > 1) // when there's just a single fragment, it corresponds to full solution
|
---|
721 | longrangeData.erase(remove_iter, longrangeData.end());
|
---|
722 |
|
---|
723 | // Final phase: sum up and print result
|
---|
724 | IndexedVectors::indices_t implicit_indices;
|
---|
725 | if (params.UseImplicitCharges.get()) {
|
---|
726 | // place all in implicit charges that are not selected but contained in ParticleRegistry
|
---|
727 | const World &world = const_cast<const World &>(World::getInstance());
|
---|
728 | const ParticleRegistry ®istry = const_cast<const ParticleRegistry &>(ParticleRegistry::getInstance());
|
---|
729 | const World::ConstAtomComposite &atoms = world.getAllAtoms();
|
---|
730 | for (World::ConstAtomComposite::const_iterator iter = atoms.begin();
|
---|
731 | iter != atoms.end(); ++iter) {
|
---|
732 | const atomId_t atomid = (*iter)->getId();
|
---|
733 | if (!world.isAtomSelected(atomid)) {
|
---|
734 | const std::string &symbol = (*iter)->getElement().getSymbol();
|
---|
735 | if (registry.isPresentByName(symbol))
|
---|
736 | implicit_indices.push_back(atomid);
|
---|
737 | }
|
---|
738 | }
|
---|
739 | LOG(2, "INFO: We added " << implicit_indices.size() << " indices due to implicit charges.");
|
---|
740 | }
|
---|
741 |
|
---|
742 | FragmentationLongRangeResults longrangeresults(
|
---|
743 | shortrangedata, longrangeData, keysets, forcekeysets);
|
---|
744 | {
|
---|
745 | SamplingGrid zero_globalgrid(domain);
|
---|
746 | longrangeresults(
|
---|
747 | shortrangedata,
|
---|
748 | longrangeData,
|
---|
749 | fullsolutionData,
|
---|
750 | full_sample,
|
---|
751 | zero_globalgrid,
|
---|
752 | implicit_indices);
|
---|
753 | printReceivedFullResults(longrangeresults);
|
---|
754 | }
|
---|
755 |
|
---|
756 | // add long-range forces
|
---|
757 | if ( const_cast<const World &>(World::getInstance()).getAllAtoms().size() != 0) {
|
---|
758 | const IndexedVectors::indexedvectors_t longrange_forces =
|
---|
759 | boost::fusion::at_key<VMGDataFused::forces_longrange>(
|
---|
760 | longrangeresults.Result_ForcesLongRangeIntegrated_fused.back()
|
---|
761 | ).getVectors();
|
---|
762 | AddForces(longrange_forces,IsAngstroem);
|
---|
763 | } else {
|
---|
764 | LOG(1, "INFO: Full molecule not loaded, hence will not add forces to atoms.");
|
---|
765 | }
|
---|
766 |
|
---|
767 | // append all keysets to homology file
|
---|
768 | status = appendToHomologies(shortrangeresults, longrangeresults, params.DoStoreGrids.get());
|
---|
769 | } else {
|
---|
770 | // append all keysets to homology file with short-range info only (without grids)
|
---|
771 | std::map<JobId_t, VMGData> longrangeData;
|
---|
772 | FragmentationLongRangeResults longrangeresults(
|
---|
773 | shortrangedata, longrangeData, keysets, forcekeysets);
|
---|
774 | status = appendToHomologies(shortrangeresults, longrangeresults, false);
|
---|
775 | }
|
---|
776 | #else
|
---|
777 | if (DoLongrange) {
|
---|
778 | ELOG(2, "File contains long-range information but long-range analysis capability not compiled in.");
|
---|
779 | }
|
---|
780 |
|
---|
781 | // append all keysets to homology file with short-range info only (without grids)
|
---|
782 | status = appendToHomologies(shortrangeresults, false);
|
---|
783 | #endif
|
---|
784 |
|
---|
785 | // we no longer clear the container
|
---|
786 | // container.clear();
|
---|
787 |
|
---|
788 | if (status)
|
---|
789 | return Action::success;
|
---|
790 | else {
|
---|
791 | STATUS("AnalyseFragmentResultsAction failed: invalid results, failed to append to homologies.");
|
---|
792 | return Action::failure;
|
---|
793 | }
|
---|
794 | }
|
---|
795 |
|
---|
796 | ActionState::ptr FragmentationAnalyseFragmentationResultsAction::performUndo(ActionState::ptr _state) {
|
---|
797 | return Action::success;
|
---|
798 | }
|
---|
799 |
|
---|
800 | ActionState::ptr FragmentationAnalyseFragmentationResultsAction::performRedo(ActionState::ptr _state){
|
---|
801 | return Action::success;
|
---|
802 | }
|
---|
803 |
|
---|
804 | bool FragmentationAnalyseFragmentationResultsAction::canUndo() {
|
---|
805 | return false;
|
---|
806 | }
|
---|
807 |
|
---|
808 | bool FragmentationAnalyseFragmentationResultsAction::shouldUndo() {
|
---|
809 | return false;
|
---|
810 | }
|
---|
811 | /** =========== end of function ====================== */
|
---|