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 | *
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6 | *
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7 | * This file is part of MoleCuilder.
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8 | *
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9 | * MoleCuilder is free software: you can redistribute it and/or modify
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10 | * it under the terms of the GNU General Public License as published by
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11 | * the Free Software Foundation, either version 2 of the License, or
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12 | * (at your option) any later version.
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13 | *
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14 | * MoleCuilder is distributed in the hope that it will be useful,
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15 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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16 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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17 | * GNU General Public License for more details.
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18 | *
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19 | * You should have received a copy of the GNU General Public License
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20 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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21 | */
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22 |
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23 | /*
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24 | * FragmentationAutomationAction.cpp
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25 | *
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26 | * Created on: May 18, 2012
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27 | * Author: heber
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28 | */
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29 |
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30 | // include config.h
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31 | #ifdef HAVE_CONFIG_H
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32 | #include <config.h>
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33 | #endif
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34 |
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35 | #include <boost/archive/text_iarchive.hpp>
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36 | // boost asio needs specific operator new
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37 | #include <boost/asio.hpp>
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38 |
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39 | #include "CodePatterns/MemDebug.hpp"
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40 |
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41 | #include <boost/assign.hpp>
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42 |
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43 | #include "CodePatterns/Assert.hpp"
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44 | #include "CodePatterns/Info.hpp"
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45 | #include "CodePatterns/Log.hpp"
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46 | #include "JobMarket/Controller/FragmentController.hpp"
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47 | #include "JobMarket/Jobs/FragmentJob.hpp"
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48 |
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49 | #include "Atom/atom.hpp"
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50 | #include "Box.hpp"
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51 | #include "Fragmentation/EnergyMatrix.hpp"
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52 | #include "Fragmentation/ForceMatrix.hpp"
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53 | #include "Fragmentation/Fragmentation.hpp"
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54 | #include "Fragmentation/SetValues/Histogram.hpp"
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55 | #include "Fragmentation/SetValues/IndexedVectors.hpp"
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56 | #include "Fragmentation/HydrogenSaturation_enum.hpp"
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57 | #include "Fragmentation/KeySet.hpp"
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58 | #include "Fragmentation/KeySetsContainer.hpp"
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59 | #include "Fragmentation/Summation/printSum.hpp"
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60 | #include "Graph/DepthFirstSearchAnalysis.hpp"
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61 | #include "Jobs/MPQCJob.hpp"
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62 | #include "Jobs/MPQCData.hpp"
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63 | #include "Jobs/MPQCData_printKeyNames.hpp"
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64 | #include "LinearAlgebra/RealSpaceMatrix.hpp"
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65 | #ifdef HAVE_VMG
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66 | #include "Jobs/VMGJob.hpp"
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67 | #endif
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68 | #include "molecule.hpp"
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69 | #include "World.hpp"
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70 |
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71 | #include <iostream>
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72 | #include <string>
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73 | #include <vector>
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74 |
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75 | #include <boost/mpl/for_each.hpp>
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76 |
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77 | #include "Actions/FragmentationAction/FragmentationAutomationAction.hpp"
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78 |
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79 | using namespace MoleCuilder;
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80 |
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81 | using namespace boost::assign;
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82 |
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83 | // and construct the stuff
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84 | #include "FragmentationAutomationAction.def"
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85 | #include "Action_impl_pre.hpp"
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86 | /** =========== define the function ====================== */
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87 |
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88 | class controller_AddOn;
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89 |
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90 | // needs to be defined for using the FragmentController
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91 | controller_AddOn *getAddOn()
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92 | {
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93 | return NULL;
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94 | }
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95 |
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96 | const int LEVEL = 5;
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97 |
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98 | /** Creates a MPQCCommandJob with argument \a filename.
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99 | *
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100 | * @param jobs created job is added to this vector
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101 | * @param command mpqc command to execute
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102 | * @param filename filename being argument to job
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103 | * @param nextid id for this job
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104 | */
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105 | void parsejob(
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106 | std::vector<FragmentJob::ptr> &jobs,
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107 | const std::string &command,
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108 | const std::string &filename,
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109 | const JobId_t nextid)
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110 | {
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111 | std::ifstream file;
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112 | file.open(filename.c_str());
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113 | ASSERT( file.good(), "parsejob() - file "+filename+" does not exist.");
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114 | std::string output((std::istreambuf_iterator<char>(file)),
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115 | std::istreambuf_iterator<char>());
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116 | double begin[NDIM] = { 0., 0., 0. };
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117 | const RealSpaceMatrix& M = World::getInstance().getDomain().getM();
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118 | const double size = M.at(0,0);
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119 | ASSERT( M.determinant() == size*size*size,
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120 | "parsejob() - current domain matrix "+toString(M)+" is not cubic.");
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121 | const int level = LEVEL;
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122 | FragmentJob::ptr testJob( new MPQCJob(nextid, output, begin, size, level) );
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123 | jobs.push_back(testJob);
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124 | file.close();
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125 | LOG(1, "INFO: Added MPQCCommandJob from file "+filename+".");
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126 | }
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127 |
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128 | /** Helper function to get number of atoms somehow.
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129 | *
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130 | * Here, we just parse the number of lines in the adjacency file as
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131 | * it should correspond to the number of atoms, except when some atoms
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132 | * are not bonded, but then fragmentation makes no sense.
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133 | *
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134 | * @param path path to the adjacency file
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135 | */
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136 | size_t getNoAtomsFromAdjacencyFile(const std::string &path)
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137 | {
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138 | size_t NoAtoms = 0;
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139 |
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140 | // parse in special file to get atom count (from line count)
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141 | std::string filename(path);
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142 | filename += FRAGMENTPREFIX;
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143 | filename += ADJACENCYFILE;
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144 | std::ifstream adjacency(filename.c_str());
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145 | if (adjacency.fail()) {
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146 | LOG(0, endl << "getNoAtomsFromAdjacencyFile() - Unable to open " << filename << ", is the directory correct?");
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147 | return false;
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148 | }
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149 | std::string buffer;
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150 | while (getline(adjacency, buffer))
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151 | NoAtoms++;
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152 | LOG(1, "INFO: There are " << NoAtoms << " atoms.");
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153 |
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154 | return NoAtoms;
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155 | }
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156 |
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157 | /** Extracts MPQCData from received vector of FragmentResults.
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158 | *
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159 | * @param results results to extract MPQCData from
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160 | * @param fragmentData on return array filled with extracted MPQCData
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161 | */
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162 | void ConvertFragmentResultToMPQCData(
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163 | const std::vector<FragmentResult::ptr> &results,
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164 | std::vector<MPQCData> &fragmentData)
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165 | {
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166 | // extract results
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167 | fragmentData.clear();
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168 | fragmentData.reserve(results.size());
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169 |
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170 | LOG(2, "DEBUG: Parsing now through " << results.size() << " results.");
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171 | for (std::vector<FragmentResult::ptr>::const_iterator iter = results.begin();
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172 | iter != results.end(); ++iter) {
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173 | //LOG(1, "RESULT: job #"+toString((*iter)->getId())+": "+toString((*iter)->result));
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174 | MPQCData extractedData;
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175 | std::stringstream inputstream((*iter)->result);
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176 | LOG(2, "DEBUG: First 50 characters FragmentResult's string: "+(*iter)->result.substr(0, 50));
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177 | boost::archive::text_iarchive ia(inputstream);
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178 | ia >> extractedData;
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179 | LOG(1, "INFO: extracted data is " << extractedData << ".");
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180 | fragmentData.push_back(extractedData);
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181 | }
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182 |
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183 | ASSERT( results.size() == fragmentData.size(),
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184 | "ConvertFragmentResultToMPQCData() - the number of extracted data differs from the number of results.");
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185 | }
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186 |
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187 | /** Print MPQCData from received results.
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188 | *
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189 | * @param results results with ids to associate with fragment number
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190 | * @param fragmentData MPQCData resulting from the jobs
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191 | * @param KeySetFilename filename with keysets to associate forces correctly
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192 | * @param NoAtoms total number of atoms
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193 | */
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194 | bool printReceivedMPQCResults(
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195 | const std::vector<FragmentResult::ptr> &results,
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196 | const std::vector<MPQCData> &fragmentData,
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197 | const std::string &KeySetFilename,
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198 | size_t NoAtoms)
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199 | {
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200 | EnergyMatrix Energy;
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201 | EnergyMatrix EnergyFragments;
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202 | ForceMatrix Force;
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203 | ForceMatrix ForceFragments;
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204 |
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205 | // align fragments
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206 | std::map< JobId_t, size_t > MatrixNrLookup;
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207 | size_t FragmentCounter = 0;
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208 | {
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209 | // bring ids in order ...
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210 | typedef std::map< JobId_t, FragmentResult::ptr> IdResultMap_t;
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211 | IdResultMap_t IdResultMap;
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212 | for (std::vector<FragmentResult::ptr>::const_iterator iter = results.begin();
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213 | iter != results.end(); ++iter) {
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214 | #ifndef NDEBUG
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215 | std::pair< IdResultMap_t::iterator, bool> inserter =
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216 | #endif
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217 | IdResultMap.insert( make_pair((*iter)->getId(), *iter) );
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218 | ASSERT( inserter.second,
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219 | "ExtractMPQCDataFromResults() - two results have same id "
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220 | +toString((*iter)->getId())+".");
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221 | }
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222 | // ... and fill lookup
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223 | for(IdResultMap_t::const_iterator iter = IdResultMap.begin();
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224 | iter != IdResultMap.end(); ++iter)
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225 | MatrixNrLookup.insert( make_pair(iter->first, FragmentCounter++) );
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226 | }
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227 | LOG(1, "INFO: There are " << FragmentCounter << " fragments.");
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228 |
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229 | std::vector<MPQCData>::const_iterator dataiter = fragmentData.begin();
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230 | std::vector<FragmentResult::ptr>::const_iterator resultiter = results.begin();
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231 | for (; dataiter != fragmentData.end(); ++dataiter, ++resultiter) {
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232 | const MPQCData &extractedData = *dataiter;
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233 | // place results into EnergyMatrix ...
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234 | {
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235 | MatrixContainer::MatrixArray matrix;
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236 | matrix.resize(1);
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237 | matrix[0].resize(1, extractedData.energies.total);
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238 | if (!Energy.AddMatrix(
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239 | std::string("MPQCJob ")+toString((*resultiter)->getId()),
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240 | matrix,
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241 | MatrixNrLookup[(*resultiter)->getId()])) {
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242 | ELOG(1, "Adding energy matrix failed.");
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243 | return false;
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244 | }
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245 | }
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246 | // ... and ForceMatrix (with two empty columns in front)
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247 | {
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248 | MatrixContainer::MatrixArray matrix;
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249 | const size_t rows = extractedData.forces.size();
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250 | matrix.resize(rows);
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251 | for (size_t i=0;i<rows;++i) {
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252 | const size_t columns = 2+extractedData.forces[i].size();
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253 | matrix[i].resize(columns, 0.);
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254 | // for (size_t j=0;j<2;++j)
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255 | // matrix[i][j] = 0.;
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256 | for (size_t j=2;j<columns;++j)
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257 | matrix[i][j] = extractedData.forces[i][j-2];
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258 | }
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259 | if (!Force.AddMatrix(
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260 | std::string("MPQCJob ")+toString((*resultiter)->getId()),
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261 | matrix,
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262 | MatrixNrLookup[(*resultiter)->getId()])) {
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263 | ELOG(1, "Adding force matrix failed.");
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264 | return false;
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265 | }
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266 | }
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267 | }
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268 | // add one more matrix (not required for energy)
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269 | MatrixContainer::MatrixArray matrix;
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270 | matrix.resize(1);
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271 | matrix[0].resize(1, 0.);
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272 | if (!Energy.AddMatrix(std::string("MPQCJob total"), matrix, FragmentCounter))
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273 | return false;
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274 | // but for energy because we need to know total number of atoms
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275 | matrix.resize(NoAtoms);
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276 | for (size_t i = 0; i< NoAtoms; ++i)
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277 | matrix[i].resize(2+NDIM, 0.);
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278 | if (!Force.AddMatrix(std::string("MPQCJob total"), matrix, FragmentCounter))
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279 | return false;
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280 |
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281 | // initialise indices
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282 | KeySetsContainer KeySet;
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283 | if (!Energy.InitialiseIndices()) return false;
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284 |
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285 | if (!Force.ParseIndices(KeySetFilename.c_str())) return false;
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286 |
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287 | if (!KeySet.ParseKeySets(KeySetFilename.c_str(), Force.RowCounter, Force.MatrixCounter)) return false;
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288 |
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289 | /// prepare for OrthogonalSummation
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290 |
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291 | // gather all present indices in AllIndices
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292 | IndexSet::ptr AllIndices(new IndexSet);
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293 | for (KeySetsContainer::ArrayOfIntVectors::const_iterator iter = KeySet.KeySets.begin();
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294 | iter != KeySet.KeySets.end(); ++iter)
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295 | for(KeySetsContainer::IntVector::const_iterator keyiter = (*iter).begin();
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296 | keyiter != (*iter).end(); ++keyiter) {
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297 | if (*keyiter != -1)
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298 | (*AllIndices) += *keyiter;
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299 | }
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300 | LOG(1, "INFO: AllIndices is " << AllIndices << ".");
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301 | // create container with all keysets
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302 | IndexSetContainer::ptr container(new IndexSetContainer(AllIndices));
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303 | for (KeySetsContainer::ArrayOfIntVectors::const_iterator iter = KeySet.KeySets.begin();
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304 | iter != KeySet.KeySets.end(); ++iter) {
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305 | IndexSet tempset;
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306 | for(KeySetsContainer::IntVector::const_iterator keyiter = (*iter).begin();
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307 | keyiter != (*iter).end(); ++keyiter)
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308 | if (*keyiter != -1)
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309 | tempset += *keyiter;
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310 | container->insert(tempset);
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311 | }
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312 | // create the map of all keysets
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313 | SubsetMap::ptr subsetmap(new SubsetMap(*container));
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314 |
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315 | /// convert all MPQCData to MPQCDataMap_t
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316 | {
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317 | // energy_t
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318 | std::vector<MPQCDataEnergyMap_t> MPQCData_Energy_fused;
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319 | MPQCData_Energy_fused.reserve(fragmentData.size());
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320 | for(std::vector<MPQCData>::const_iterator dataiter = fragmentData.begin();
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321 | dataiter != fragmentData.end(); ++dataiter) {
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322 | const MPQCData &extractedData = *dataiter;
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323 | LOG(2, "DEBUG: Current extracted Data is " << extractedData << ".");
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324 | MPQCDataEnergyMap_t instance;
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325 | boost::fusion::at_key<MPQCDataFused::energy_total>(instance) = extractedData.energies.total;
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326 | boost::fusion::at_key<MPQCDataFused::energy_nuclear_repulsion>(instance) = extractedData.energies.nuclear_repulsion;
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327 | boost::fusion::at_key<MPQCDataFused::energy_electron_coulomb>(instance) = extractedData.energies.electron_coulomb;
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328 | boost::fusion::at_key<MPQCDataFused::energy_electron_exchange>(instance) = extractedData.energies.electron_exchange;
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329 | boost::fusion::at_key<MPQCDataFused::energy_correlation>(instance) = extractedData.energies.correlation;
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330 | boost::fusion::at_key<MPQCDataFused::energy_overlap>(instance) = extractedData.energies.overlap;
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331 | boost::fusion::at_key<MPQCDataFused::energy_kinetic>(instance) = extractedData.energies.kinetic;
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332 | boost::fusion::at_key<MPQCDataFused::energy_hcore>(instance) = extractedData.energies.hcore;
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333 | boost::fusion::at_key<MPQCDataFused::energy_eigenvalues>(instance) = extractedData.energies.eigenvalues;
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334 | MPQCData_Energy_fused.push_back(instance);
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335 | }
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336 |
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337 | // forces
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338 | const IndexSetContainer::Container_t &indices = container->getContainer();
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339 | ASSERT( indices.size() == fragmentData.size(),
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340 | "FragmentationAutomationAction::performCall() - indices and fragmentData differ in size.");
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341 | std::vector<MPQCDataForceMap_t> MPQCData_Force_fused;
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342 | MPQCData_Force_fused.reserve(fragmentData.size());
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343 | std::vector<MPQCData>::const_iterator dataiter = fragmentData.begin();
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344 | IndexSetContainer::Container_t::const_iterator indexiter = indices.begin();
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345 | for(;dataiter != fragmentData.end(); ++dataiter, ++indexiter) {
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346 | const MPQCData &extractedData = *dataiter;
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347 | LOG(2, "DEBUG: Current extracted Data is " << extractedData << ".");
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348 | MPQCDataForceMap_t instance;
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349 | boost::fusion::at_key<MPQCDataFused::forces>(instance) =
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350 | IndexedVectors(**indexiter, extractedData.forces);
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351 | MPQCData_Force_fused.push_back(instance);
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352 | }
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353 |
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354 | // times
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355 | std::vector<MPQCDataTimeMap_t> MPQCData_Time_fused;
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356 | MPQCData_Time_fused.reserve(fragmentData.size());
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357 | for(std::vector<MPQCData>::const_iterator dataiter = fragmentData.begin();
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358 | dataiter != fragmentData.end(); ++dataiter) {
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359 | const MPQCData &extractedData = *dataiter;
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360 | LOG(2, "DEBUG: Current extracted Data is " << extractedData << ".");
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361 | MPQCDataTimeMap_t instance;
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362 | boost::fusion::at_key<MPQCDataFused::times_walltime>(instance) = extractedData.times.walltime;
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363 | boost::fusion::at_key<MPQCDataFused::times_cputime>(instance) = extractedData.times.cputime;
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364 | boost::fusion::at_key<MPQCDataFused::times_flops>(instance) = extractedData.times.flops;
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365 | MPQCData_Time_fused.push_back(instance);
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366 | }
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367 |
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368 | // create a vector of all job ids
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369 | std::vector<JobId_t> jobids(results.size(), JobId::IllegalJob);
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370 | std::transform(results.begin(), results.end(), jobids.begin(),
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371 | boost::bind(&FragmentResult::getId,
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372 | boost::bind(&FragmentResult::ptr::operator->, _1)));
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373 |
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374 | // sum up and print energies
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375 | boost::mpl::for_each<MPQCDataEnergyVector_t>(
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376 | printSum<MPQCDataEnergyMap_t>(
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377 | subsetmap,
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378 | MPQCData_Energy_fused,
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379 | jobids,
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380 | container->getContainer(),
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381 | MatrixNrLookup)
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382 | );
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383 |
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384 | // sum up and print forces
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385 | boost::mpl::for_each<MPQCDataForceVector_t>(
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386 | printSum<MPQCDataForceMap_t>(
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387 | subsetmap,
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388 | MPQCData_Force_fused,
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389 | jobids,
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390 | container->getContainer(),
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391 | MatrixNrLookup)
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392 | );
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393 |
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394 | // TODO: Times should just be summed not orthogonalized
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395 | // // sum up and print times
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396 | // boost::mpl::for_each<MPQCDataTimeVector_t>(
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397 | // printSum<MPQCDataTimeMap_t>(
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398 | // subsetmap,
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399 | // MPQCData_Time_fused,
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400 | // jobids,
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401 | // container->getContainer(),
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402 | // MatrixNrLookup)
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403 | // );
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404 | }
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405 |
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406 | // combine all found data
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407 | if (!KeySet.ParseManyBodyTerms()) return false;
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408 |
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409 | if (!EnergyFragments.AllocateMatrix(Energy.Header, Energy.MatrixCounter, Energy.RowCounter, Energy.ColumnCounter)) return false;
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410 | if (!ForceFragments.AllocateMatrix(Force.Header, Force.MatrixCounter, Force.RowCounter, Force.ColumnCounter)) return false;
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411 |
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412 | if(!Energy.SetLastMatrix(0., 0)) return false;
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413 | if(!Force.SetLastMatrix(0., 2)) return false;
|
---|
414 |
|
---|
415 | for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
|
---|
416 | // --------- sum up energy --------------------
|
---|
417 | LOG(1, "INFO: Summing energy of order " << BondOrder+1 << " ...");
|
---|
418 | if (!EnergyFragments.SumSubManyBodyTerms(Energy, KeySet, BondOrder)) return false;
|
---|
419 | if (!Energy.SumSubEnergy(EnergyFragments, NULL, KeySet, BondOrder, 1.)) return false;
|
---|
420 |
|
---|
421 | // --------- sum up Forces --------------------
|
---|
422 | LOG(1, "INFO: Summing forces of order " << BondOrder+1 << " ...");
|
---|
423 | if (!ForceFragments.SumSubManyBodyTerms(Force, KeySet, BondOrder)) return false;
|
---|
424 | if (!Force.SumSubForces(ForceFragments, KeySet, BondOrder, 1.)) return false;
|
---|
425 | }
|
---|
426 |
|
---|
427 | // for debugging print resulting energy and forces
|
---|
428 | LOG(1, "INFO: Resulting energy is " << Energy.Matrix[ FragmentCounter ][0][0]);
|
---|
429 | std::stringstream output;
|
---|
430 | for (int i=0; i< Force.RowCounter[FragmentCounter]; ++i) {
|
---|
431 | for (int j=0; j< Force.ColumnCounter[FragmentCounter]; ++j)
|
---|
432 | output << Force.Matrix[ FragmentCounter ][i][j] << " ";
|
---|
433 | output << "\n";
|
---|
434 | }
|
---|
435 | LOG(1, "INFO: Resulting forces are " << std::endl << output.str());
|
---|
436 |
|
---|
437 | return true;
|
---|
438 | }
|
---|
439 |
|
---|
440 |
|
---|
441 | void RunService(
|
---|
442 | boost::asio::io_service &io_service,
|
---|
443 | std::string message)
|
---|
444 | {
|
---|
445 | message = std::string("io_service: ") + message;
|
---|
446 | io_service.reset();
|
---|
447 | Info info(message.c_str());
|
---|
448 | io_service.run();
|
---|
449 | }
|
---|
450 |
|
---|
451 | void requestIds(
|
---|
452 | FragmentController &controller,
|
---|
453 | const FragmentationFragmentationAutomationAction::FragmentationFragmentationAutomationParameters ¶ms,
|
---|
454 | const size_t numberjobs)
|
---|
455 | {
|
---|
456 | controller.requestIds(params.host.get(), params.port.get(), numberjobs);
|
---|
457 | }
|
---|
458 |
|
---|
459 | bool createJobsFromFiles(
|
---|
460 | FragmentController &controller,
|
---|
461 | const FragmentationFragmentationAutomationAction::FragmentationFragmentationAutomationParameters ¶ms,
|
---|
462 | const std::vector< boost::filesystem::path > &jobfiles)
|
---|
463 | {
|
---|
464 | std::vector<FragmentJob::ptr> jobs;
|
---|
465 | for (std::vector< boost::filesystem::path >::const_iterator iter = jobfiles.begin();
|
---|
466 | iter != jobfiles .end(); ++iter) {
|
---|
467 | const std::string &filename = (*iter).string();
|
---|
468 | if (boost::filesystem::exists(filename)) {
|
---|
469 | const JobId_t next_id = controller.getAvailableId();
|
---|
470 | LOG(1, "INFO: Creating MPQCCommandJob with filename'"
|
---|
471 | +filename+"', and id "+toString(next_id)+".");
|
---|
472 | parsejob(jobs, params.executable.get().string(), filename, next_id);
|
---|
473 | } else {
|
---|
474 | ELOG(1, "Fragment job "+filename+" does not exist.");
|
---|
475 | return false;
|
---|
476 | }
|
---|
477 | }
|
---|
478 | controller.addJobs(jobs);
|
---|
479 | controller.sendJobs(params.host.get(), params.port.get());
|
---|
480 | return true;
|
---|
481 | }
|
---|
482 |
|
---|
483 | #ifdef HAVE_VMG
|
---|
484 | bool createLongRangeJobs(
|
---|
485 | FragmentController &controller,
|
---|
486 | const FragmentationFragmentationAutomationAction::FragmentationFragmentationAutomationParameters ¶ms,
|
---|
487 | const std::vector<MPQCData> &fragmentData)
|
---|
488 | {
|
---|
489 | std::vector<FragmentJob::ptr> jobs;
|
---|
490 | // add one job for each fragment as the short-range correction which we need
|
---|
491 | // to subtract from the obtained full potential to get the long-range part only
|
---|
492 | for (std::vector<MPQCData>::const_iterator iter = fragmentData.begin();
|
---|
493 | iter != fragmentData.end(); ++iter) {
|
---|
494 | const JobId_t next_id = controller.getAvailableId();
|
---|
495 | LOG(1, "INFO: Creating VMGJob.");
|
---|
496 | FragmentJob::ptr testJob(
|
---|
497 | new VMGJob(next_id, iter->sampled_grid) );
|
---|
498 | jobs.push_back(testJob);
|
---|
499 | }
|
---|
500 |
|
---|
501 | // add one more job for the full calculation
|
---|
502 | // TODO: Here, we actually have to combine all the other sampled_grids
|
---|
503 | {
|
---|
504 | const int level = LEVEL;
|
---|
505 | const int GRID = pow(2, level);
|
---|
506 | std::vector<double> full_sample(GRID*GRID*GRID, 0.);
|
---|
507 | double begin[NDIM] = { 0., 0., 0. };
|
---|
508 | const RealSpaceMatrix& M = World::getInstance().getDomain().getM();
|
---|
509 | const double size = M.at(0,0);
|
---|
510 | ASSERT( M.determinant() == size*size*size,
|
---|
511 | "createLongRangeJobs() - current domain matrix "+toString(M)+" is not cubic.");
|
---|
512 | const SamplingGrid full_sampled_grid(begin, size, level, full_sample);
|
---|
513 | const JobId_t next_id = controller.getAvailableId();
|
---|
514 | FragmentJob::ptr testJob(
|
---|
515 | new VMGJob(next_id, full_sampled_grid) );
|
---|
516 | jobs.push_back(testJob);
|
---|
517 | }
|
---|
518 |
|
---|
519 | // then send jobs to controller
|
---|
520 | controller.addJobs(jobs);
|
---|
521 | controller.sendJobs(params.host.get(), params.port.get());
|
---|
522 | return true;
|
---|
523 | }
|
---|
524 | #endif
|
---|
525 |
|
---|
526 | void WaitforResults(
|
---|
527 | boost::asio::io_service &io_service,
|
---|
528 | FragmentController &controller,
|
---|
529 | const FragmentationFragmentationAutomationAction::FragmentationFragmentationAutomationParameters ¶ms,
|
---|
530 | const size_t NoExpectedResults
|
---|
531 | )
|
---|
532 | {
|
---|
533 | size_t NoCalculatedResults = 0;
|
---|
534 | while (NoCalculatedResults != NoExpectedResults) {
|
---|
535 | // wait a bit
|
---|
536 | boost::asio::deadline_timer timer(io_service);
|
---|
537 | timer.expires_from_now(boost::posix_time::milliseconds(500));
|
---|
538 | timer.wait();
|
---|
539 | // then request status
|
---|
540 | controller.checkResults(params.host.get(), params.port.get());
|
---|
541 | RunService(io_service, "Checking on results");
|
---|
542 |
|
---|
543 | const std::pair<size_t, size_t> JobStatus = controller.getJobStatus();
|
---|
544 | LOG(1, "INFO: #" << JobStatus.first << " are waiting in the queue and #" << JobStatus.second << " jobs are calculated so far.");
|
---|
545 | NoCalculatedResults = JobStatus.second;
|
---|
546 | }
|
---|
547 | }
|
---|
548 |
|
---|
549 |
|
---|
550 | Action::state_ptr FragmentationFragmentationAutomationAction::performCall() {
|
---|
551 | boost::asio::io_service io_service;
|
---|
552 | FragmentController controller(io_service);
|
---|
553 |
|
---|
554 | // TODO: Have io_service run in second thread and merge with current again eventually
|
---|
555 |
|
---|
556 | // Phase One: obtain ids
|
---|
557 | std::vector< boost::filesystem::path > jobfiles = params.jobfiles.get();
|
---|
558 | requestIds(controller, params, jobfiles.size());
|
---|
559 | RunService(io_service, "Requesting ids");
|
---|
560 |
|
---|
561 | // Phase Two: create and add MPQCJobs
|
---|
562 | if (!createJobsFromFiles(controller, params, jobfiles))
|
---|
563 | return Action::failure;
|
---|
564 | RunService(io_service, "Adding MPQCJobs");
|
---|
565 |
|
---|
566 | // Phase Three: calculate result
|
---|
567 | WaitforResults(io_service, controller, params, jobfiles.size());
|
---|
568 | controller.receiveResults(params.host.get(), params.port.get());
|
---|
569 | RunService(io_service, "Requesting short-range results");
|
---|
570 | std::vector<FragmentResult::ptr> MPQCresults = controller.getReceivedResults();
|
---|
571 | std::vector<MPQCData> fragmentData;
|
---|
572 | ConvertFragmentResultToMPQCData(MPQCresults, fragmentData);
|
---|
573 |
|
---|
574 | // print intermediate short-range results
|
---|
575 | {
|
---|
576 | LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
|
---|
577 | printReceivedMPQCResults(
|
---|
578 | MPQCresults,
|
---|
579 | fragmentData,
|
---|
580 | params.path.get(),
|
---|
581 | getNoAtomsFromAdjacencyFile(params.path.get()));
|
---|
582 | }
|
---|
583 |
|
---|
584 | #ifdef HAVE_VMG
|
---|
585 | if (params.DoLongrange.get()) {
|
---|
586 | // Phase Four: obtain more ids
|
---|
587 | requestIds(controller, params, fragmentData.size()+1);
|
---|
588 | RunService(io_service, "Requesting ids");
|
---|
589 |
|
---|
590 | // Phase Five: create VMGJobs
|
---|
591 | if (!createLongRangeJobs(controller, params, fragmentData))
|
---|
592 | return Action::failure;
|
---|
593 | RunService(io_service, "Adding VMGJobs");
|
---|
594 |
|
---|
595 | // Phase Six: calculate result
|
---|
596 | WaitforResults(io_service, controller, params, fragmentData.size()+1);
|
---|
597 | controller.receiveResults(params.host.get(), params.port.get());
|
---|
598 | RunService(io_service, "Requesting long-range results");
|
---|
599 | std::vector<FragmentResult::ptr> VMGresults = controller.getReceivedResults();
|
---|
600 | ASSERT( MPQCresults.size()+1 == VMGresults.size(),
|
---|
601 | "FragmentationFragmentationAutomationAction::performCall() - number of MPQCresultd and VMGresults don't match.");
|
---|
602 |
|
---|
603 | // Final phase: print result
|
---|
604 | {
|
---|
605 | LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
|
---|
606 | printReceivedMPQCResults(
|
---|
607 | MPQCresults,
|
---|
608 | fragmentData,
|
---|
609 | params.path.get(),
|
---|
610 | getNoAtomsFromAdjacencyFile(params.path.get()));
|
---|
611 | }
|
---|
612 | }
|
---|
613 | #endif
|
---|
614 | size_t Exitflag = controller.getExitflag();
|
---|
615 |
|
---|
616 | return (Exitflag == 0) ? Action::success : Action::failure;
|
---|
617 | }
|
---|
618 |
|
---|
619 | Action::state_ptr FragmentationFragmentationAutomationAction::performUndo(Action::state_ptr _state) {
|
---|
620 | return Action::success;
|
---|
621 | }
|
---|
622 |
|
---|
623 | Action::state_ptr FragmentationFragmentationAutomationAction::performRedo(Action::state_ptr _state){
|
---|
624 | return Action::success;
|
---|
625 | }
|
---|
626 |
|
---|
627 | bool FragmentationFragmentationAutomationAction::canUndo() {
|
---|
628 | return false;
|
---|
629 | }
|
---|
630 |
|
---|
631 | bool FragmentationFragmentationAutomationAction::shouldUndo() {
|
---|
632 | return false;
|
---|
633 | }
|
---|
634 | /** =========== end of function ====================== */
|
---|