[edecba] | 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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[94d5ac6] | 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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[edecba] | 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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[6ca578] | 41 | #include <boost/assign.hpp>
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| 42 |
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| 43 | #include "CodePatterns/Assert.hpp"
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[edecba] | 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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[d12d621] | 50 | #include "Box.hpp"
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[edecba] | 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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[e06820] | 54 | #include "Fragmentation/SetValues/Histogram.hpp"
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[e13990b] | 55 | #include "Fragmentation/SetValues/IndexedVectors.hpp"
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[edecba] | 56 | #include "Fragmentation/HydrogenSaturation_enum.hpp"
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[6ca578] | 57 | #include "Fragmentation/KeySet.hpp"
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[edecba] | 58 | #include "Fragmentation/KeySetsContainer.hpp"
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[286e36] | 59 | #include "Fragmentation/Summation/printSum.hpp"
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[edecba] | 60 | #include "Graph/DepthFirstSearchAnalysis.hpp"
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[28e894] | 61 | #include "Jobs/MPQCJob.hpp"
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[4bc75d] | 62 | #include "Jobs/MPQCData.hpp"
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[1f66c7] | 63 | #include "Jobs/MPQCData_printKeyNames.hpp"
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[d12d621] | 64 | #include "LinearAlgebra/RealSpaceMatrix.hpp"
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[69c733] | 65 | #ifdef HAVE_VMG
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| 66 | #include "Jobs/VMGJob.hpp"
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| 67 | #endif
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[edecba] | 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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[8cae4c] | 75 | #include <boost/mpl/for_each.hpp>
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| 76 |
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[edecba] | 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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[6ca578] | 81 | using namespace boost::assign;
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| 82 |
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[edecba] | 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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[d12d621] | 96 | const int LEVEL = 5;
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| 97 |
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[edecba] | 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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[d12d621] | 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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[edecba] | 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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[2764e0] | 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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[edecba] | 186 |
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| 187 | /** Print MPQCData from received results.
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| 188 | *
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[2764e0] | 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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[edecba] | 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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[2764e0] | 196 | const std::vector<MPQCData> &fragmentData,
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[edecba] | 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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[d12d621] | 219 | "ExtractMPQCDataFromResults() - two results have same id "
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[edecba] | 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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[2764e0] | 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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[edecba] | 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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[a9558f] | 237 | matrix[0].resize(1, extractedData.energies.total);
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[edecba] | 238 | if (!Energy.AddMatrix(
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[2764e0] | 239 | std::string("MPQCJob ")+toString((*resultiter)->getId()),
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[edecba] | 240 | matrix,
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[2764e0] | 241 | MatrixNrLookup[(*resultiter)->getId()])) {
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[edecba] | 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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[2764e0] | 260 | std::string("MPQCJob ")+toString((*resultiter)->getId()),
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[edecba] | 261 | matrix,
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[2764e0] | 262 | MatrixNrLookup[(*resultiter)->getId()])) {
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[edecba] | 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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[6ca578] | 281 | // initialise indices
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| 282 | KeySetsContainer KeySet;
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[edecba] | 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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[6ca578] | 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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[e13990b] | 315 | /// convert all MPQCData to MPQCDataMap_t
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[8cae4c] | 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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[adccae] | 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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[8cae4c] | 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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[dde8ec] | 333 | boost::fusion::at_key<MPQCDataFused::energy_eigenvalues>(instance) = extractedData.energies.eigenvalues;
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[8cae4c] | 334 | MPQCData_Energy_fused.push_back(instance);
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| 335 | }
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[965e2f] | 336 |
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[8cae4c] | 337 | // forces
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[e13990b] | 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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[8cae4c] | 341 | std::vector<MPQCDataForceMap_t> MPQCData_Force_fused;
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| 342 | MPQCData_Force_fused.reserve(fragmentData.size());
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[e13990b] | 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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[8cae4c] | 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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[e13990b] | 349 | boost::fusion::at_key<MPQCDataFused::forces>(instance) =
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| 350 | IndexedVectors(**indexiter, extractedData.forces);
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[8cae4c] | 351 | MPQCData_Force_fused.push_back(instance);
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| 352 | }
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[6ca578] | 353 |
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[8cae4c] | 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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[e13990b] | 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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[8cae4c] | 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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[56df37] | 405 |
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[6ca578] | 406 | // combine all found data
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[edecba] | 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 |
|
---|
| 412 | if(!Energy.SetLastMatrix(0., 0)) return false;
|
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| 413 | if(!Force.SetLastMatrix(0., 2)) return false;
|
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| 414 |
|
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| 415 | for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
|
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| 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 |
|
---|
[c5324f] | 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 | }
|
---|
[edecba] | 450 |
|
---|
[c5324f] | 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;
|
---|
[edecba] | 476 | }
|
---|
| 477 | }
|
---|
[c5324f] | 478 | controller.addJobs(jobs);
|
---|
| 479 | controller.sendJobs(params.host.get(), params.port.get());
|
---|
| 480 | return true;
|
---|
| 481 | }
|
---|
| 482 |
|
---|
[69c733] | 483 | #ifdef HAVE_VMG
|
---|
| 484 | bool createLongRangeJobs(
|
---|
| 485 | FragmentController &controller,
|
---|
| 486 | const FragmentationFragmentationAutomationAction::FragmentationFragmentationAutomationParameters ¶ms,
|
---|
[d12d621] | 487 | const std::vector<MPQCData> &fragmentData)
|
---|
[69c733] | 488 | {
|
---|
| 489 | std::vector<FragmentJob::ptr> jobs;
|
---|
[d12d621] | 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) {
|
---|
[69c733] | 494 | const JobId_t next_id = controller.getAvailableId();
|
---|
| 495 | LOG(1, "INFO: Creating VMGJob.");
|
---|
[d12d621] | 496 | FragmentJob::ptr testJob(
|
---|
[28c025] | 497 | new VMGJob(next_id, iter->sampled_grid) );
|
---|
[69c733] | 498 | jobs.push_back(testJob);
|
---|
| 499 | }
|
---|
[d12d621] | 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);
|
---|
[28c025] | 506 | std::vector<double> full_sample(GRID*GRID*GRID, 0.);
|
---|
[d12d621] | 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.");
|
---|
[28c025] | 512 | const SamplingGrid full_sampled_grid(begin, size, level, full_sample);
|
---|
[d12d621] | 513 | const JobId_t next_id = controller.getAvailableId();
|
---|
| 514 | FragmentJob::ptr testJob(
|
---|
[28c025] | 515 | new VMGJob(next_id, full_sampled_grid) );
|
---|
[d12d621] | 516 | jobs.push_back(testJob);
|
---|
| 517 | }
|
---|
| 518 |
|
---|
| 519 | // then send jobs to controller
|
---|
[69c733] | 520 | controller.addJobs(jobs);
|
---|
| 521 | controller.sendJobs(params.host.get(), params.port.get());
|
---|
| 522 | return true;
|
---|
| 523 | }
|
---|
| 524 | #endif
|
---|
| 525 |
|
---|
[c5324f] | 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 | {
|
---|
[edecba] | 533 | size_t NoCalculatedResults = 0;
|
---|
[c5324f] | 534 | while (NoCalculatedResults != NoExpectedResults) {
|
---|
[edecba] | 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
|
---|
[bd81f9] | 540 | controller.checkResults(params.host.get(), params.port.get());
|
---|
[c5324f] | 541 | RunService(io_service, "Checking on results");
|
---|
| 542 |
|
---|
[edecba] | 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 | }
|
---|
[c5324f] | 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 |
|
---|
[69c733] | 561 | // Phase Two: create and add MPQCJobs
|
---|
[c5324f] | 562 | if (!createJobsFromFiles(controller, params, jobfiles))
|
---|
| 563 | return Action::failure;
|
---|
[69c733] | 564 | RunService(io_service, "Adding MPQCJobs");
|
---|
[c5324f] | 565 |
|
---|
| 566 | // Phase Three: calculate result
|
---|
| 567 | WaitforResults(io_service, controller, params, jobfiles.size());
|
---|
[bd81f9] | 568 | controller.receiveResults(params.host.get(), params.port.get());
|
---|
[69c733] | 569 | RunService(io_service, "Requesting short-range results");
|
---|
[2764e0] | 570 | std::vector<FragmentResult::ptr> MPQCresults = controller.getReceivedResults();
|
---|
| 571 | std::vector<MPQCData> fragmentData;
|
---|
| 572 | ConvertFragmentResultToMPQCData(MPQCresults, fragmentData);
|
---|
[c5324f] | 573 |
|
---|
[69c733] | 574 | // print intermediate short-range results
|
---|
[edecba] | 575 | {
|
---|
[bd81f9] | 576 | LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
|
---|
[edecba] | 577 | printReceivedMPQCResults(
|
---|
[69c733] | 578 | MPQCresults,
|
---|
[2764e0] | 579 | fragmentData,
|
---|
[bd81f9] | 580 | params.path.get(),
|
---|
| 581 | getNoAtomsFromAdjacencyFile(params.path.get()));
|
---|
[edecba] | 582 | }
|
---|
[69c733] | 583 |
|
---|
| 584 | #ifdef HAVE_VMG
|
---|
| 585 | if (params.DoLongrange.get()) {
|
---|
| 586 | // Phase Four: obtain more ids
|
---|
[2764e0] | 587 | requestIds(controller, params, fragmentData.size()+1);
|
---|
[69c733] | 588 | RunService(io_service, "Requesting ids");
|
---|
| 589 |
|
---|
| 590 | // Phase Five: create VMGJobs
|
---|
[d12d621] | 591 | if (!createLongRangeJobs(controller, params, fragmentData))
|
---|
[69c733] | 592 | return Action::failure;
|
---|
| 593 | RunService(io_service, "Adding VMGJobs");
|
---|
| 594 |
|
---|
| 595 | // Phase Six: calculate result
|
---|
[2764e0] | 596 | WaitforResults(io_service, controller, params, fragmentData.size()+1);
|
---|
[69c733] | 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();
|
---|
[2764e0] | 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 | }
|
---|
[69c733] | 612 | }
|
---|
| 613 | #endif
|
---|
[edecba] | 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 ====================== */
|
---|