| 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,
 | 
|---|
| 401 | //            container->getContainer(),
 | 
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| 402 | //            MatrixNrLookup)
 | 
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| 403 | //        );
 | 
|---|
| 404 |   }
 | 
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| 405 | 
 | 
|---|
| 406 |   // combine all found data
 | 
|---|
| 407 |   if (!KeySet.ParseManyBodyTerms()) return false;
 | 
|---|
| 408 | 
 | 
|---|
| 409 |   if (!EnergyFragments.AllocateMatrix(Energy.Header, Energy.MatrixCounter, Energy.RowCounter, Energy.ColumnCounter)) return false;
 | 
|---|
| 410 |   if (!ForceFragments.AllocateMatrix(Force.Header, Force.MatrixCounter, Force.RowCounter, Force.ColumnCounter)) return false;
 | 
|---|
| 411 | 
 | 
|---|
| 412 |   if(!Energy.SetLastMatrix(0., 0)) return false;
 | 
|---|
| 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 ====================== */
 | 
|---|