[a3427f] | 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) 2013 University of Bonn. All rights reserved.
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[5aaa43] | 5 | * Copyright (C) 2013 Frederik Heber. All rights reserved.
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[a3427f] | 6 | *
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| 7 | *
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| 8 | * This file is part of MoleCuilder.
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| 9 | *
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| 10 | * MoleCuilder is free software: you can redistribute it and/or modify
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| 11 | * it under the terms of the GNU General Public License as published by
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| 12 | * the Free Software Foundation, either version 2 of the License, or
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| 13 | * (at your option) any later version.
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| 14 | *
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| 15 | * MoleCuilder is distributed in the hope that it will be useful,
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| 16 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 17 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 18 | * GNU General Public License for more details.
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| 19 | *
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| 20 | * You should have received a copy of the GNU General Public License
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| 21 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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| 22 | */
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| 23 |
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| 24 | /*
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| 25 | * AnalyseFragmentationResultsAction.cpp
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| 26 | *
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| 27 | * Created on: Mar 8, 2013
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| 28 | * Author: heber
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| 29 | */
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| 30 |
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| 31 | // include config.h
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| 32 | #ifdef HAVE_CONFIG_H
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| 33 | #include <config.h>
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| 34 | #endif
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| 35 |
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| 36 | // include headers that implement a archive in simple text format
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| 37 | // and before MemDebug due to placement new
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| 38 | #include <boost/archive/text_oarchive.hpp>
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| 39 | #include <boost/archive/text_iarchive.hpp>
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| 40 |
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| 41 | #include "CodePatterns/MemDebug.hpp"
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| 42 |
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[e5ebaf] | 43 | #include <boost/foreach.hpp>
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[a3427f] | 44 | #include <boost/mpl/remove.hpp>
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| 45 |
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| 46 | #include <vector>
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| 47 | #include <fstream>
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| 48 | #include <iostream>
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| 49 | #include <string>
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| 50 | #include <vector>
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| 51 |
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| 52 | #include "CodePatterns/Assert.hpp"
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| 53 | #include "CodePatterns/Log.hpp"
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| 54 |
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| 55 | #ifdef HAVE_JOBMARKET
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| 56 | #include "JobMarket/types.hpp"
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| 57 | #else
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| 58 | typedef size_t JobId_t;
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| 59 | #endif
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| 60 |
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[e5ebaf] | 61 | #include "Descriptors/AtomIdDescriptor.hpp"
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[a3427f] | 62 | #include "Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp"
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| 63 | #include "Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp"
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| 64 | #include "Fragmentation/Summation/Containers/FragmentationResultContainer.hpp"
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| 65 | #include "Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp"
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| 66 | #include "Fragmentation/Summation/Containers/MPQCData.hpp"
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| 67 | #include "Fragmentation/Summation/Containers/MPQCData_printKeyNames.hpp"
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| 68 | #include "Fragmentation/Homology/HomologyContainer.hpp"
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| 69 | #include "Fragmentation/Homology/HomologyGraph.hpp"
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| 70 | #include "Fragmentation/KeySetsContainer.hpp"
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[5c867e] | 71 | #include "Fragmentation/Summation/SetValues/Eigenvalues.hpp"
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[a3427f] | 72 | #include "Fragmentation/Summation/SetValues/Fragment.hpp"
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| 73 | #include "Fragmentation/Summation/SetValues/Histogram.hpp"
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| 74 | #include "Fragmentation/Summation/SetValues/IndexedVectors.hpp"
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| 75 | #include "Fragmentation/Summation/IndexSetContainer.hpp"
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| 76 | #include "Fragmentation/Summation/writeTable.hpp"
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| 77 | #ifdef HAVE_VMG
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| 78 | #include "Fragmentation/Summation/Containers/VMGData.hpp"
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| 79 | #include "Fragmentation/Summation/Containers/VMGDataFused.hpp"
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| 80 | #include "Fragmentation/Summation/Containers/VMGDataMap.hpp"
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| 81 | #include "Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp"
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| 82 | #endif
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[e5ebaf] | 83 | #include "Helpers/defs.hpp"
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[a3427f] | 84 | #include "World.hpp"
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| 85 |
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| 86 | #include "Actions/FragmentationAction/AnalyseFragmentationResultsAction.hpp"
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| 87 |
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| 88 | using namespace MoleCuilder;
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| 89 |
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| 90 | // and construct the stuff
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| 91 | #include "AnalyseFragmentationResultsAction.def"
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| 92 | #include "Action_impl_pre.hpp"
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| 93 | /** =========== define the function ====================== */
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| 94 |
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| 95 | void writeToFile(const std::string &filename, const std::string contents)
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| 96 | {
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| 97 | std::ofstream tablefile(filename.c_str());
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| 98 | tablefile << contents;
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| 99 | tablefile.close();
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| 100 | }
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| 101 |
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| 102 | /** Print (short range) energy, forces, and timings from received results.
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| 103 | *
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| 104 | * @param results summed up results container
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| 105 | */
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| 106 | void printReceivedShortResults(
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| 107 | const FragmentationShortRangeResults &results)
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| 108 | {
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| 109 | // print tables (without eigenvalues, they go extra)
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| 110 | {
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[5c867e] | 111 | typedef boost::mpl::remove<
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| 112 | boost::mpl::remove<MPQCDataEnergyVector_t, MPQCDataFused::energy_eigenvalues>::type,
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| 113 | MPQCDataFused::energy_eigenhistogram>::type
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[a3427f] | 114 | MPQCDataEnergyVector_noeigenvalues_t;
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| 115 | const std::string energyresult =
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| 116 | writeTable<MPQCDataEnergyMap_t, MPQCDataEnergyVector_noeigenvalues_t >()(
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| 117 | results.Result_Energy_fused, results.getMaxLevel());
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[1b5a40] | 118 | LOG(2, "DEBUG: Energy table is \n" << energyresult);
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[a3427f] | 119 | std::string filename;
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| 120 | filename += FRAGMENTPREFIX + std::string("_Energy.dat");
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| 121 | writeToFile(filename, energyresult);
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| 122 | }
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| 123 |
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[5c867e] | 124 | {
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| 125 | typedef boost::mpl::list<
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| 126 | MPQCDataFused::energy_eigenvalues
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| 127 | > MPQCDataEigenvalues_t;
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| 128 | const std::string eigenvalueresult =
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| 129 | writeTable<MPQCDataEnergyMap_t, MPQCDataEigenvalues_t >()(
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| 130 | results.Result_Energy_fused, results.getMaxLevel());
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[1b5a40] | 131 | LOG(2, "DEBUG: Eigenvalue table is \n" << eigenvalueresult);
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[5c867e] | 132 | std::string filename;
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| 133 | filename += FRAGMENTPREFIX + std::string("_Eigenvalues.dat");
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| 134 | writeToFile(filename, eigenvalueresult);
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| 135 | }
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| 136 |
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| 137 | {
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| 138 | typedef boost::mpl::list<
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| 139 | MPQCDataFused::energy_eigenhistogram
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| 140 | > MPQCDataEigenhistogram_t;
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| 141 | const std::string eigenhistogramresult =
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| 142 | writeTable<MPQCDataEnergyMap_t, MPQCDataEigenhistogram_t >()(
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| 143 | results.Result_Energy_fused, results.getMaxLevel());
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[1b5a40] | 144 | LOG(2, "DEBUG: Eigenhistogram table is \n" << eigenhistogramresult);
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[5c867e] | 145 | std::string filename;
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| 146 | filename += FRAGMENTPREFIX + std::string("_Eigenhistogram.dat");
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| 147 | writeToFile(filename, eigenhistogramresult);
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| 148 | }
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| 149 |
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[a3427f] | 150 | {
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| 151 | typedef boost::mpl::list<
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| 152 | MPQCDataFused::energy_eigenvalues
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| 153 | > MPQCDataEigenvalues_t;
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| 154 | const std::string eigenvalueresult =
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| 155 | writeTable<MPQCDataEnergyMap_t, MPQCDataEigenvalues_t >()(
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| 156 | results.Result_Energy_fused, results.getMaxLevel());
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[1b5a40] | 157 | LOG(2, "DEBUG: Eigenvalue table is \n" << eigenvalueresult);
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[a3427f] | 158 | std::string filename;
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| 159 | filename += FRAGMENTPREFIX + std::string("_Eigenvalues.dat");
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| 160 | writeToFile(filename, eigenvalueresult);
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| 161 | }
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| 162 |
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| 163 | {
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| 164 | const std::string forceresult =
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| 165 | writeTable<MPQCDataForceMap_t, MPQCDataForceVector_t>()(
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| 166 | results.Result_Force_fused, results.getMaxLevel());
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[1b5a40] | 167 | LOG(2, "DEBUG: Force table is \n" << forceresult);
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[a3427f] | 168 | std::string filename;
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| 169 | filename += FRAGMENTPREFIX + std::string("_Forces.dat");
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| 170 | writeToFile(filename, forceresult);
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| 171 | }
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| 172 | // we don't want to print grid to a table
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| 173 | {
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| 174 | // print times (without flops for now)
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| 175 | typedef boost::mpl::remove<
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| 176 | boost::mpl::remove<MPQCDataTimeVector_t, MPQCDataFused::times_total_flops>::type,
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| 177 | MPQCDataFused::times_gather_flops>::type
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| 178 | MPQCDataTimeVector_noflops_t;
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| 179 | const std::string timesresult =
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| 180 | writeTable<MPQCDataTimeMap_t, MPQCDataTimeVector_noflops_t >()(
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| 181 | results.Result_Time_fused, results.getMaxLevel());
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[1b5a40] | 182 | LOG(2, "DEBUG: Times table is \n" << timesresult);
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[a3427f] | 183 | std::string filename;
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| 184 | filename += FRAGMENTPREFIX + std::string("_Times.dat");
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| 185 | writeToFile(filename, timesresult);
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| 186 | }
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| 187 | }
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| 188 |
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| 189 |
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| 190 | /** Print long range energy from received results.
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| 191 | *
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| 192 | * @param results summed up results container
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| 193 | */
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| 194 | void printReceivedFullResults(
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| 195 | const FragmentationLongRangeResults &results)
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| 196 | {
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| 197 | // print tables (without eigenvalues, they go extra)
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| 198 |
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| 199 | if (results.Result_LongRange_fused.size() >= (results.getMaxLevel()-2))
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| 200 | {
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| 201 | const std::string gridresult =
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| 202 | writeTable<VMGDataMap_t, VMGDataVector_t >()(
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| 203 | results.Result_LongRange_fused, results.getMaxLevel(), 2);
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[1b5a40] | 204 | LOG(2, "DEBUG: VMG table is \n" << gridresult);
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[a3427f] | 205 | std::string filename;
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| 206 | filename += FRAGMENTPREFIX + std::string("_VMGEnergy.dat");
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| 207 | writeToFile(filename, gridresult);
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| 208 | }
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| 209 |
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| 210 | if (results.Result_LongRangeIntegrated_fused.size() >= (results.getMaxLevel()-2))
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| 211 | {
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| 212 | const std::string gridresult =
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| 213 | writeTable<VMGDataLongRangeMap_t, VMGDataLongRangeVector_t >()(
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| 214 | results.Result_LongRangeIntegrated_fused, results.getMaxLevel(), 2);
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[1b5a40] | 215 | LOG(2, "DEBUG: LongRange table is \n" << gridresult);
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[a3427f] | 216 | std::string filename;
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| 217 | filename += FRAGMENTPREFIX + std::string("_LongRangeEnergy.dat");
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| 218 | writeToFile(filename, gridresult);
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| 219 | }
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| 220 | }
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| 221 |
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| 222 | bool appendToHomologyFile(
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| 223 | const boost::filesystem::path &homology_file,
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| 224 | const FragmentationShortRangeResults &shortrangeresults,
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| 225 | const FragmentationLongRangeResults &longrangeresults
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| 226 | )
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| 227 | {
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| 228 | /// read homology container (if present)
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| 229 | HomologyContainer homology_container;
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| 230 | if (boost::filesystem::exists(homology_file)) {
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| 231 | std::ifstream returnstream(homology_file.string().c_str());
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| 232 | if (returnstream.good()) {
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| 233 | boost::archive::text_iarchive ia(returnstream);
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| 234 | ia >> homology_container;
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| 235 | } else {
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| 236 | ELOG(2, "Failed to parse from " << homology_file.string() << ".");
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| 237 | }
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| 238 | returnstream.close();
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| 239 | } else {
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| 240 | LOG(2, "Could not open " << homology_file.string()
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| 241 | << ", creating empty container.");
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| 242 | }
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| 243 |
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| 244 | /// append all fragments to a HomologyContainer
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| 245 | HomologyContainer::container_t values;
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| 246 |
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| 247 | // convert KeySetContainer to IndexSetContainer
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| 248 | IndexSetContainer::ptr ForceContainer(new IndexSetContainer(shortrangeresults.getForceKeySet()));
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| 249 | const IndexSetContainer::Container_t &Indices = shortrangeresults.getContainer();
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| 250 | const IndexSetContainer::Container_t &ForceIndices = ForceContainer->getContainer();
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| 251 | IndexSetContainer::Container_t::const_iterator iter = Indices.begin();
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| 252 | IndexSetContainer::Container_t::const_iterator forceiter = ForceIndices.begin();
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[e5ebaf] | 253 |
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[a3427f] | 254 | /// go through all fragments
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| 255 | for (;iter != Indices.end(); ++iter, ++forceiter) // go through each IndexSet
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| 256 | {
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| 257 | /// create new graph entry in HomologyContainer which is (key,value) type
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| 258 | LOG(1, "INFO: Creating new graph with " << **forceiter << ".");
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| 259 | HomologyGraph graph(**forceiter);
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| 260 | LOG(2, "DEBUG: Created graph " << graph << ".");
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| 261 | const IndexSet::ptr &index = *iter;
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| 262 | HomologyContainer::value_t value;
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| 263 |
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| 264 | // obtain fragment as key
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| 265 | std::map<IndexSet::ptr, std::pair< MPQCDataFragmentMap_t, MPQCDataFragmentMap_t> >::const_iterator fragmentiter
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| 266 | = longrangeresults.Result_perIndexSet_Fragment.find(index);
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| 267 | ASSERT( fragmentiter != longrangeresults.Result_perIndexSet_Fragment.end(),
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| 268 | "appendToHomologyFile() - cannot find index "+toString(*index)
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| 269 | +" in FragmentResults.");
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| 270 | value.first = boost::fusion::at_key<MPQCDataFused::fragment>(fragmentiter->second.first);
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| 271 |
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| 272 | // obtain energy as value
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| 273 | std::map<IndexSet::ptr, std::pair< MPQCDataEnergyMap_t, MPQCDataEnergyMap_t> >::const_iterator energyiter
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| 274 | = shortrangeresults.Result_perIndexSet_Energy.find(index);
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| 275 | ASSERT( energyiter != shortrangeresults.Result_perIndexSet_Energy.end(),
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| 276 | "appendToHomologyFile() - cannot find index "+toString(*index)
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| 277 | +" in FragmentResults.");
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| 278 | // value.second = boost::fusion::at_key<MPQCDataFused::energy_total>(energyiter->second.first); // values
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| 279 | value.second = boost::fusion::at_key<MPQCDataFused::energy_total>(energyiter->second.second); // contributions
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| 280 | values.insert( std::make_pair( graph, value) );
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| 281 | }
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| 282 | homology_container.insert(values);
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| 283 |
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[1b5a40] | 284 | if (DoLog(2)) {
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| 285 | LOG(2, "DEBUG: Listing all present atomic ids ...");
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| 286 | std::stringstream output;
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| 287 | for (World::AtomIterator iter = World::getInstance().getAtomIter();
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| 288 | iter != World::getInstance().atomEnd(); ++iter)
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| 289 | output << (*iter)->getId() << " ";
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| 290 | LOG(2, "DEBUG: { " << output.str() << "} .");
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| 291 | }
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[a3427f] | 292 |
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| 293 | // for debugging: print container
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[1b5a40] | 294 | if (DoLog(2)) {
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| 295 | LOG(2, "DEBUG: Listing all present homologies ...");
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| 296 | for (HomologyContainer::container_t::const_iterator iter =
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| 297 | homology_container.begin(); iter != homology_container.end(); ++iter) {
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| 298 | LOG(2, "DEBUG: graph " << iter->first << " has Fragment "
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| 299 | << iter->second.first << " and associated energy " << iter->second.second << ".");
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| 300 | }
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[a3427f] | 301 | }
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| 302 |
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| 303 | /// store homology container again
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| 304 | std::ofstream outputstream(homology_file.string().c_str());
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| 305 | if (outputstream.good()) { // check if opened
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| 306 | boost::archive::text_oarchive oa(outputstream);
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| 307 | oa << homology_container;
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| 308 | if (outputstream.fail()) { // check if correctly written
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| 309 | LOG(1, "Failed to write to file " << homology_file.string() << ".");
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| 310 | return false;
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| 311 | } else
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| 312 | outputstream.close();
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| 313 | } else {
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| 314 | LOG(1, "Failed to open file " << homology_file.string()
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| 315 | << " for writing.");
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| 316 | return false;
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| 317 | }
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| 318 | return true;
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| 319 | }
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| 320 |
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| 321 | Action::state_ptr FragmentationAnalyseFragmentationResultsAction::performCall() {
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| 322 |
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[55e1bc] | 323 | // if file is given, parse from file into resultscontainer
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[a3427f] | 324 | FragmentationResultContainer& container = FragmentationResultContainer::getInstance();
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[55e1bc] | 325 | if (!params.resultsfile.get().empty()) {
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| 326 | boost::filesystem::path resultsfile = params.resultsfile.get();
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| 327 | if (boost::filesystem::exists(resultsfile)) {
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| 328 | LOG(1, "INFO: Parsing results from " << resultsfile.string() << ".");
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| 329 | std::ifstream returnstream(resultsfile.string().c_str());
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| 330 | if (returnstream.good()) {
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| 331 | boost::archive::text_iarchive ia(returnstream);
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| 332 | ia >> container;
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| 333 | }
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| 334 | } else {
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| 335 | ELOG(1, "Given file" << resultsfile.string() << " does not exist.");
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| 336 | }
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| 337 | }
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| 338 |
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| 339 | // get data and keysets from ResultsContainer
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[a3427f] | 340 | const std::map<JobId_t, MPQCData> &shortrangedata = container.getShortRangeResults();
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| 341 | const KeySetsContainer &keysets = container.getKeySets();
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| 342 | const KeySetsContainer &forcekeysets = container.getForceKeySets();
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| 343 | const bool DoLongrange = container.areFullRangeResultsPresent();
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[e5ebaf] | 344 | const bool IsAngstroem = true;
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[a3427f] | 345 |
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[55e1bc] | 346 | if (keysets.KeySets.empty()) {
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| 347 | ELOG(2, "There are no results in the container.");
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| 348 | return Action::failure;
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| 349 | }
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| 350 |
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[a3427f] | 351 | FragmentationShortRangeResults shortrangeresults(shortrangedata, keysets, forcekeysets);
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| 352 | shortrangeresults(shortrangedata);
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| 353 | printReceivedShortResults(shortrangeresults);
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| 354 |
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[e5ebaf] | 355 | // adding obtained forces
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| 356 | if ( World::getInstance().getAllAtoms().size() != 0) {
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| 357 | const IndexedVectors::indexedvectors_t forces =
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| 358 | boost::fusion::at_key<MPQCDataFused::forces>(
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| 359 | shortrangeresults.Result_Force_fused.back()
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| 360 | ).getVectors();
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| 361 | ;
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| 362 | for(IndexedVectors::indexedvectors_t::const_iterator iter = forces.begin();
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| 363 | iter != forces.end(); ++iter) {
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| 364 | const IndexedVectors::index_t &index = iter->first;
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| 365 | const IndexedVectors::vector_t &forcevector = iter->second;
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| 366 | ASSERT( forcevector.size() == NDIM,
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| 367 | "printReceivedShortResults() - obtained force vector has incorrect dimension.");
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| 368 | // note that mpqc calculates a gradient, hence force pointing into opposite direction
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| 369 | // we have to mind different units here: MPQC has a_o, while we may have angstroem
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| 370 | Vector ForceVector(-forcevector[0], -forcevector[1], -forcevector[2]);
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| 371 | if (IsAngstroem)
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| 372 | for (size_t i=0;i<NDIM;++i)
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| 373 | ForceVector[i] *= AtomicLengthToAngstroem;
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| 374 | atom *_atom = World::getInstance().getAtom(AtomById(index));
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| 375 | if(_atom != NULL)
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| 376 | _atom->setAtomicForce(_atom->getAtomicForce() + ForceVector);
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| 377 | else
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| 378 | ELOG(2, "Could not find atom to id " << index << ".");
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| 379 | }
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| 380 | } else {
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| 381 | LOG(1, "INFO: Full molecule not loaded, hence will not add forces to atoms.");
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| 382 | }
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| 383 |
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[a3427f] | 384 | #ifdef HAVE_VMG
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| 385 | if (DoLongrange) {
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| 386 | if ( World::getInstance().getAllAtoms().size() == 0) {
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| 387 | ELOG(1, "Please load the full molecule into the world before starting this action.");
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| 388 | return Action::failure;
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| 389 | }
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| 390 |
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| 391 | FragmentationChargeDensity summedChargeDensity(shortrangedata,keysets);
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| 392 | const std::vector<SamplingGrid> full_sample = summedChargeDensity.getFullSampledGrid();
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| 393 |
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| 394 | std::map<JobId_t, VMGData> longrangeData = container.getLongRangeResults();
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| 395 | // remove full solution corresponding to full_sample from map (must be highest ids), has to be treated extra
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| 396 | std::map<JobId_t, VMGData>::iterator iter = longrangeData.end();
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| 397 | for (size_t i=0;i<full_sample.size();++i)
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| 398 | --iter;
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| 399 | std::map<JobId_t, VMGData>::iterator remove_iter = iter;
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| 400 | std::vector<VMGData> fullsolutionData;
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| 401 | for (; iter != longrangeData.end(); ++iter)
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| 402 | fullsolutionData.push_back(iter->second);
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| 403 | longrangeData.erase(remove_iter, longrangeData.end());
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| 404 |
|
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| 405 | // Final phase: sum up and print result
|
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| 406 | FragmentationLongRangeResults longrangeresults(
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| 407 | shortrangedata,longrangeData,keysets, forcekeysets);
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| 408 | longrangeresults(
|
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| 409 | shortrangedata,
|
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| 410 | longrangeData,
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| 411 | fullsolutionData,
|
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| 412 | full_sample);
|
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| 413 | printReceivedFullResults(longrangeresults);
|
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| 414 |
|
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| 415 | // append all keysets to homology file
|
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| 416 | if (!params.homology_file.get().empty()) {
|
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| 417 | const boost::filesystem::path &homology_file = params.homology_file.get();
|
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| 418 | if (homology_file.string() != "") {
|
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| 419 | LOG(1, "INFO: Appending HomologyGraphs to file " << homology_file.string() << ".");
|
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| 420 | if (!appendToHomologyFile(homology_file, shortrangeresults, longrangeresults))
|
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| 421 | return Action::failure;
|
---|
| 422 | }
|
---|
| 423 | }
|
---|
| 424 | }
|
---|
[e2925fd] | 425 | #else
|
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| 426 | if (DoLongrange)
|
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| 427 | ELOG(2, "File contains long-range information but long-range analysis capability not compiled in.");
|
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[a3427f] | 428 | #endif
|
---|
| 429 |
|
---|
| 430 | container.clear();
|
---|
| 431 |
|
---|
| 432 | return Action::success;
|
---|
| 433 | }
|
---|
| 434 |
|
---|
| 435 | Action::state_ptr FragmentationAnalyseFragmentationResultsAction::performUndo(Action::state_ptr _state) {
|
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| 436 | return Action::success;
|
---|
| 437 | }
|
---|
| 438 |
|
---|
| 439 | Action::state_ptr FragmentationAnalyseFragmentationResultsAction::performRedo(Action::state_ptr _state){
|
---|
| 440 | return Action::success;
|
---|
| 441 | }
|
---|
| 442 |
|
---|
| 443 | bool FragmentationAnalyseFragmentationResultsAction::canUndo() {
|
---|
| 444 | return false;
|
---|
| 445 | }
|
---|
| 446 |
|
---|
| 447 | bool FragmentationAnalyseFragmentationResultsAction::shouldUndo() {
|
---|
| 448 | return false;
|
---|
| 449 | }
|
---|
| 450 | /** =========== end of function ====================== */
|
---|