[8aa597] | 1 | /*
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| 2 | * Project: MoleCuilder
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| 3 | * Description: creates and alters molecular systems
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| 4 | * Copyright (C) 2012 University of Bonn. All rights reserved.
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[5aaa43] | 5 | * Copyright (C) 2013 Frederik Heber. All rights reserved.
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[8aa597] | 6 | * Please see the COPYING file or "Copyright notice" in builder.cpp for details.
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| 7 | *
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| 8 | *
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| 9 | * This file is part of MoleCuilder.
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| 10 | *
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| 11 | * MoleCuilder is free software: you can redistribute it and/or modify
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| 12 | * it under the terms of the GNU General Public License as published by
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| 13 | * the Free Software Foundation, either version 2 of the License, or
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| 14 | * (at your option) any later version.
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| 15 | *
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| 16 | * MoleCuilder is distributed in the hope that it will be useful,
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| 17 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 18 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 19 | * GNU General Public License for more details.
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| 20 | *
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| 21 | * You should have received a copy of the GNU General Public License
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| 22 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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| 23 | */
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| 24 |
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| 25 | /*
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| 26 | * Extractors.cpp
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| 27 | *
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| 28 | * Created on: 15.10.2012
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| 29 | * Author: heber
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| 30 | */
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| 31 |
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| 32 | // include config.h
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| 33 | #ifdef HAVE_CONFIG_H
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| 34 | #include <config.h>
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| 35 | #endif
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| 36 |
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| 37 | #include "CodePatterns/MemDebug.hpp"
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| 38 |
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[caa00e9] | 39 | #include <sstream>
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[8aa597] | 40 | #include <utility>
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| 41 | #include <vector>
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| 42 | #include <boost/assign.hpp>
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[64bdfd] | 43 | #include <boost/bind.hpp>
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[caa00e9] | 44 | #include <boost/foreach.hpp>
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[8aa597] | 45 |
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[301dbf] | 46 | #include "CodePatterns/Assert.hpp"
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[51e0e3] | 47 | #include "CodePatterns/IteratorAdaptors.hpp"
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[8aa597] | 48 | #include "CodePatterns/Log.hpp"
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[51e0e3] | 49 | #include "CodePatterns/toString.hpp"
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[8aa597] | 50 |
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| 51 | #include "LinearAlgebra/Vector.hpp"
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| 52 |
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| 53 | #include "FunctionApproximation/Extractors.hpp"
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| 54 | #include "FunctionApproximation/FunctionArgument.hpp"
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| 55 |
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| 56 | using namespace boost::assign;
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| 57 |
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| 58 | FunctionModel::arguments_t
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[49f163] | 59 | Extractors::gatherAllDistanceArguments(
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[691be4] | 60 | const Fragment::positions_t& positions,
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| 61 | const Fragment::charges_t& charges,
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[8aa597] | 62 | const size_t globalid)
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| 63 | {
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| 64 | FunctionModel::arguments_t result;
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| 65 |
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| 66 | // go through current configuration and gather all other distances
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| 67 | Fragment::positions_t::const_iterator firstpositer = positions.begin();
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| 68 | for (;firstpositer != positions.end(); ++firstpositer) {
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| 69 | Fragment::positions_t::const_iterator secondpositer = positions.begin();//firstpositer;
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| 70 | for (; secondpositer != positions.end(); ++secondpositer) {
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| 71 | if (firstpositer == secondpositer)
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| 72 | continue;
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| 73 | argument_t arg;
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| 74 | const Vector firsttemp((*firstpositer)[0],(*firstpositer)[1],(*firstpositer)[2]);
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| 75 | const Vector secondtemp((*secondpositer)[0],(*secondpositer)[1],(*secondpositer)[2]);
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[49f163] | 76 | arg.distance = firsttemp.distance(secondtemp);
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[691be4] | 77 | arg.types = std::make_pair(
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| 78 | charges[ std::distance(positions.begin(), firstpositer) ],
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| 79 | charges[ std::distance(positions.begin(), secondpositer) ]
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| 80 | );
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[49f163] | 81 | arg.indices = std::make_pair(
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| 82 | std::distance(
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| 83 | positions.begin(), firstpositer),
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| 84 | std::distance(
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| 85 | positions.begin(), secondpositer)
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| 86 | );
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| 87 | arg.globalid = globalid;
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| 88 | result.push_back(arg);
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| 89 | }
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| 90 | }
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| 91 |
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| 92 | return result;
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| 93 | }
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| 94 |
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| 95 | FunctionModel::arguments_t
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| 96 | Extractors::gatherAllSymmetricDistanceArguments(
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[691be4] | 97 | const Fragment::positions_t& positions,
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| 98 | const Fragment::charges_t& charges,
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[49f163] | 99 | const size_t globalid)
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| 100 | {
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| 101 | FunctionModel::arguments_t result;
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| 102 |
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| 103 | // go through current configuration and gather all other distances
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| 104 | Fragment::positions_t::const_iterator firstpositer = positions.begin();
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| 105 | for (;firstpositer != positions.end(); ++firstpositer) {
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| 106 | Fragment::positions_t::const_iterator secondpositer = firstpositer;
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| 107 | for (; secondpositer != positions.end(); ++secondpositer) {
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| 108 | if (firstpositer == secondpositer)
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| 109 | continue;
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| 110 | argument_t arg;
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| 111 | const Vector firsttemp((*firstpositer)[0],(*firstpositer)[1],(*firstpositer)[2]);
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| 112 | const Vector secondtemp((*secondpositer)[0],(*secondpositer)[1],(*secondpositer)[2]);
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[8aa597] | 113 | arg.distance = firsttemp.distance(secondtemp);
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[691be4] | 114 | arg.types = std::make_pair(
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| 115 | charges[ std::distance(positions.begin(), firstpositer) ],
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| 116 | charges[ std::distance(positions.begin(), secondpositer) ]
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| 117 | );
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[8aa597] | 118 | arg.indices = std::make_pair(
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| 119 | std::distance(
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| 120 | positions.begin(), firstpositer),
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| 121 | std::distance(
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| 122 | positions.begin(), secondpositer)
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| 123 | );
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| 124 | arg.globalid = globalid;
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[31a2be] | 125 | LOG(3, "DEBUG: Created argument " << arg << ".");
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[8aa597] | 126 | result.push_back(arg);
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| 127 | }
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| 128 | }
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| 129 |
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| 130 | return result;
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| 131 | }
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| 132 |
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[691be4] | 133 | Fragment::positions_t Extractors::_detail::gatherPositionsFromTargets(
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| 134 | const Fragment::positions_t& positions,
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| 135 | const Fragment::charges_t& charges,
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| 136 | const chargeiters_t &targets
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[301dbf] | 137 | )
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| 138 | {
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| 139 | Fragment::positions_t filtered_positions;
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| 140 | for (chargeiters_t::const_iterator firstpairiter = targets.begin();
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| 141 | firstpairiter != targets.end(); ++firstpairiter) {
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| 142 | Fragment::positions_t::const_iterator positer = positions.begin();
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| 143 | const size_t steps = std::distance(charges.begin(), *firstpairiter);
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| 144 | std::advance(positer, steps);
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| 145 | filtered_positions.push_back(*positer);
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| 146 | }
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| 147 | return filtered_positions;
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| 148 | }
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| 149 |
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[691be4] | 150 | FunctionModel::arguments_t Extractors::_detail::gatherDistancesFromTargets(
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| 151 | const Fragment::positions_t& positions,
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| 152 | const Fragment::charges_t& charges,
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| 153 | const chargeiters_t &targets,
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| 154 | const size_t globalid
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| 155 | )
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| 156 | {
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| 157 | Fragment::positions_t filtered_positions;
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| 158 | Fragment::charges_t filtered_charges;
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| 159 | for (chargeiters_t::const_iterator firstpairiter = targets.begin();
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| 160 | firstpairiter != targets.end(); ++firstpairiter) {
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| 161 | Fragment::positions_t::const_iterator positer = positions.begin();
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| 162 | const size_t steps = std::distance(charges.begin(), *firstpairiter);
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| 163 | std::advance(positer, steps);
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| 164 | filtered_positions.push_back(*positer);
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| 165 | filtered_charges.push_back(**firstpairiter);
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| 166 | }
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| 167 | return Extractors::gatherAllSymmetricDistanceArguments(
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| 168 | filtered_positions,
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| 169 | filtered_charges,
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| 170 | globalid);
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| 171 | }
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| 172 |
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[bc6705] | 173 | Extractors::elementcounts_t
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| 174 | Extractors::_detail::getElementCounts(
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| 175 | const Fragment::charges_t elements
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| 176 | )
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| 177 | {
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| 178 | elementcounts_t elementcounts;
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| 179 | for (Fragment::charges_t::const_iterator elementiter = elements.begin();
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| 180 | elementiter != elements.end(); ++elementiter) {
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| 181 | // insert new element
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| 182 | std::pair< elementcounts_t::iterator, bool> inserter =
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| 183 | elementcounts.insert( std::make_pair( *elementiter, 1) );
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| 184 | // if already present, just increase its count
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| 185 | if (!inserter.second)
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| 186 | ++(inserter.first->second);
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| 187 | }
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| 188 | return elementcounts;
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| 189 | }
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| 190 |
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[c211f7] | 191 | Extractors::elementtargets_t
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| 192 | Extractors::_detail::convertElementcountsToTargets(
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| 193 | const Fragment::charges_t &charges,
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| 194 | const elementcounts_t &elementcounts
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| 195 | )
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| 196 | {
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[301dbf] | 197 | elementtargets_t elementtargets;
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| 198 | for (elementcounts_t::const_iterator countiter = elementcounts.begin();
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| 199 | countiter != elementcounts.end();
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| 200 | ++countiter) {
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| 201 | chargeiter_t chargeiter = charges.begin();
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| 202 | const element_t &element = countiter->first;
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| 203 | const count_t &count = countiter->second;
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| 204 | for (count_t i = 0; i < count; ++i) {
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| 205 | chargeiter_t tempiter = std::find(chargeiter, charges.end(), element);
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| 206 | if (tempiter != charges.end()) {
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| 207 | // try to insert new list
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| 208 | std::pair< elementtargets_t::iterator, bool> inserter =
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| 209 | elementtargets.insert( std::make_pair( countiter->first, chargeiters_t(1, tempiter)) );
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| 210 | // if already present, append to it
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| 211 | if (!inserter.second) {
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| 212 | inserter.first->second.push_back(tempiter);
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| 213 | } else { // if created, increase vector's reserve to known size
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| 214 | inserter.first->second.reserve(countiter->second);
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| 215 | }
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| 216 | // search from this element onwards then
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| 217 | chargeiter = ++tempiter;
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| 218 | } else {
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[57f14c] | 219 | ELOG(1, "Could not find desired number " << count << " of element "
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| 220 | << element << " in fragment with " << charges << ".");
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[c211f7] | 221 | return Extractors::elementtargets_t();
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[301dbf] | 222 | }
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| 223 | }
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| 224 | }
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[c211f7] | 225 | return elementtargets;
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| 226 | }
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| 227 |
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[caa00e9] | 228 | Extractors::elementtargets_t
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| 229 | Extractors::_detail::convertChargesToTargetMap(
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| 230 | const Fragment::charges_t& charges,
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| 231 | Fragment::charges_t elements
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| 232 | )
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| 233 | {
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| 234 | // place each charge into a map
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| 235 | elementtargets_t completeelementtargets;
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| 236 | for (chargeiter_t chargeiter = charges.begin();
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| 237 | chargeiter != charges.end();
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| 238 | ++chargeiter) {
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| 239 | std::pair< elementtargets_t::iterator, bool> inserter =
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| 240 | completeelementtargets.insert( std::make_pair( *chargeiter, chargeiters_t(1, chargeiter)) );
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| 241 | // if already present, append to it
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| 242 | if (!inserter.second) {
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| 243 | inserter.first->second.push_back(chargeiter);
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| 244 | }
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| 245 | }
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| 246 | // pick out desired charges only
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| 247 | std::sort(elements.begin(), elements.end());
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| 248 | Fragment::charges_t::iterator eraseiter =
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| 249 | std::unique(elements.begin(), elements.end());
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| 250 | elements.erase(eraseiter, elements.end());
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| 251 | elementtargets_t elementtargets;
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| 252 | for(Fragment::charges_t::const_iterator iter = elements.begin();
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| 253 | iter != elements.end();
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| 254 | ++iter) {
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| 255 | elementtargets_t::const_iterator finditer = completeelementtargets.find(*iter);
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| 256 | ASSERT( finditer != completeelementtargets.end(),
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| 257 | "Extractors::_detail::convertChargesToTargetMap() - no element "+toString(*iter)+" present?");
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| 258 | std::pair< elementtargets_t::iterator, bool> inserter =
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| 259 | elementtargets.insert( std::make_pair( finditer->first, finditer->second) );
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| 260 | ASSERT( inserter.second,
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| 261 | "Extractors::_detail::convertChargesToTargetMap() - key twice?");
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| 262 | }
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| 263 | return elementtargets;
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| 264 | }
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| 265 |
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| 266 |
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[63e786] | 267 | Extractors::chargeiters_t
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| 268 | Extractors::_detail::realignElementtargets(
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| 269 | const elementtargets_t &elementtargets,
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| 270 | const Fragment::charges_t elements,
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| 271 | const elementcounts_t &elementcounts
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| 272 | )
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| 273 | {
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| 274 | chargeiters_t targets;
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| 275 | elementcounts_t counts; // how many chargeiters of this element have been used
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[caa00e9] | 276 | if (!elements.empty()) { // skip if no elements given
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| 277 | targets.reserve(elements.size());
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| 278 | for (Fragment::charges_t::const_iterator elementiter = elements.begin();
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| 279 | elementiter != elements.end(); ++elementiter) {
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| 280 | const element_t &element = *elementiter;
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| 281 | count_t &count = counts[element]; // if not present, std::map creates instances with default of 0
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[63e786] | 282 | #ifndef NDEBUG
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[caa00e9] | 283 | {
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| 284 | elementcounts_t::const_iterator testiter = elementcounts.find(element);
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| 285 | ASSERT( (testiter != elementcounts.end()) && (count < testiter->second),
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| 286 | "Extractors::_detail::realignElementTargets() - we want to use more chargeiters for element "
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| 287 | +toString(element)+" than we counted initially.");
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| 288 | }
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[63e786] | 289 | #endif
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[caa00e9] | 290 | elementtargets_t::const_iterator targetiter = elementtargets.find(element);
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| 291 | if (targetiter != elementtargets.end()) {
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| 292 | const chargeiters_t &chargeiters = targetiter->second;
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| 293 | const chargeiter_t &chargeiter = chargeiters[count++];
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| 294 | targets.push_back(chargeiter);
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| 295 | }
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| 296 | }
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[63e786] | 297 | }
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| 298 | return targets;
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| 299 | }
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| 300 |
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[caa00e9] | 301 | FunctionModel::arguments_t
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| 302 | Extractors::gatherAllDistancesFromFragment(
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| 303 | const Fragment::positions_t& positions,
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| 304 | const Fragment::charges_t& charges,
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| 305 | const Fragment::charges_t elements,
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| 306 | const size_t globalid
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| 307 | )
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| 308 | {
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| 309 | /// The main problem here is that we have to know how many same
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| 310 | /// elements (but different atoms!) we are required to find. Hence,
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| 311 | /// we first have to count same elements, then get different targets
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| 312 | /// for each and then associated them in correct order back again.
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| 313 |
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[8203ce8] | 314 | // 0. if no elements given, we return empty arguments
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| 315 | if (elements.empty())
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| 316 | return FunctionModel::arguments_t();
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| 317 |
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[caa00e9] | 318 | // 1. we have to place each charge into a map as unique chargeiter, i.e. map
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| 319 | elementtargets_t elementtargets =
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| 320 | Extractors::_detail::convertChargesToTargetMap(
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| 321 | charges,
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| 322 | elements);
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| 323 |
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| 324 | // 2. now we have to combine elementcounts out of elementtargets per desired element
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| 325 | // in a combinatorial fashion
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| 326 | targets_per_combination_t combinations =
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| 327 | Extractors::_detail::CombineChargesAndTargets(
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| 328 | elements,
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| 329 | elementtargets);
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| 330 |
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| 331 | // 3. finally, convert chargeiters into argument list
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| 332 | FunctionModel::arguments_t args =
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| 333 | Extractors::_detail::convertTargetsToArguments(
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| 334 | positions,
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| 335 | charges,
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| 336 | combinations,
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| 337 | globalid);
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| 338 |
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| 339 | return args;
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| 340 | }
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| 341 |
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| 342 | Extractors::targets_per_combination_t
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| 343 | Extractors::_detail::CombineChargesAndTargets(
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| 344 | const Fragment::charges_t& elements,
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| 345 | const elementtargets_t& elementtargets
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| 346 | )
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| 347 | {
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| 348 | // recursively create all correct combinations of targets
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| 349 | targets_per_combination_t combinations;
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| 350 | chargeiters_t currenttargets;
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| 351 | boost::function<void (const chargeiters_t ¤ttargets)> addFunction =
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| 352 | boost::bind(&targets_per_combination_t::push_back,
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| 353 | boost::ref(combinations),
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| 354 | _1);
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| 355 | pickLastElementAsTarget(elements, elementtargets, currenttargets, addFunction);
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| 356 |
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| 357 | return combinations;
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| 358 | }
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| 359 |
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[69fcba] | 360 | const Fragment::position_t& getPositionToChargeIter(
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| 361 | const Fragment::positions_t& positions,
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| 362 | const Fragment::charges_t& charges,
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| 363 | const Extractors::chargeiter_t &iter
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| 364 | )
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| 365 | {
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| 366 | Fragment::positions_t::const_iterator positer = positions.begin();
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| 367 | std::advance(positer, std::distance(charges.begin(), iter));
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| 368 | const Fragment::position_t &position = *positer;
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| 369 | return position;
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| 370 | }
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| 371 |
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| 372 |
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[caa00e9] | 373 | FunctionModel::arguments_t
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| 374 | Extractors::_detail::convertTargetsToArguments(
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| 375 | const Fragment::positions_t& positions,
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| 376 | const Fragment::charges_t& charges,
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| 377 | const targets_per_combination_t combinations,
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| 378 | const size_t globalid
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| 379 | )
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| 380 | {
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| 381 | FunctionModel::arguments_t args;
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[69fcba] | 382 | // create arguments from each combination. We cannot use
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| 383 | // gatherallSymmetricDistanceArguments() because it would not create the
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| 384 | // correct indices.
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[caa00e9] | 385 | for (targets_per_combination_t::const_iterator iter = combinations.begin();
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| 386 | iter != combinations.end();
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| 387 | ++iter) {
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[69fcba] | 388 | for(chargeiters_t::const_iterator firstiter = iter->begin();
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| 389 | firstiter != iter->end();
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| 390 | ++firstiter) {
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| 391 | const Fragment::position_t &firstpos =
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| 392 | getPositionToChargeIter(positions, charges, *firstiter);
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| 393 | const Vector firsttemp(firstpos[0],firstpos[1],firstpos[2]);
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| 394 | for(chargeiters_t::const_iterator seconditer = firstiter;
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| 395 | seconditer != iter->end();
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| 396 | ++seconditer) {
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| 397 | if (firstiter == seconditer)
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| 398 | continue;
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| 399 | const Fragment::position_t &secondpos =
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| 400 | getPositionToChargeIter(positions, charges, *seconditer);
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| 401 | const Vector secondtemp(secondpos[0],secondpos[1],secondpos[2]);
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| 402 | argument_t arg;
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| 403 | arg.distance = firsttemp.distance(secondtemp);
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| 404 | arg.indices.first = std::distance(charges.begin(), *firstiter);
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| 405 | arg.indices.second = std::distance(charges.begin(), *seconditer);
|
---|
| 406 | arg.types.first = **firstiter;
|
---|
| 407 | arg.types.second = **seconditer;
|
---|
| 408 | args.push_back( arg );
|
---|
| 409 | }
|
---|
[caa00e9] | 410 | }
|
---|
| 411 | }
|
---|
| 412 |
|
---|
| 413 | return args;
|
---|
| 414 | }
|
---|
| 415 |
|
---|
| 416 | void
|
---|
| 417 | Extractors::_detail::pickLastElementAsTarget(
|
---|
| 418 | Fragment::charges_t elements,
|
---|
| 419 | elementtargets_t elementtargets,
|
---|
| 420 | chargeiters_t ¤ttargets,
|
---|
| 421 | boost::function<void (const chargeiters_t ¤ttargets)> &addFunction
|
---|
| 422 | )
|
---|
| 423 | {
|
---|
| 424 | // get last element from charges
|
---|
[8203ce8] | 425 | ASSERT( !elements.empty(),
|
---|
| 426 | "Extractors::_detail::pickLastElementAsTarget() - no elements given to pick targets for.");
|
---|
[caa00e9] | 427 | const Fragment::charge_t charge = elements.back();
|
---|
| 428 | elements.pop_back();
|
---|
| 429 | elementtargets_t::iterator iter = elementtargets.find(charge);
|
---|
| 430 | if (iter == elementtargets.end())
|
---|
| 431 | return;
|
---|
| 432 | bool NotEmpty = !iter->second.empty();
|
---|
| 433 | while (NotEmpty) {
|
---|
| 434 | // get last target from the vector of chargeiters
|
---|
| 435 | chargeiter_t target = iter->second.back();
|
---|
| 436 | iter->second.pop_back();
|
---|
| 437 | // remove this key if empty
|
---|
| 438 | if (iter->second.empty()) {
|
---|
| 439 | elementtargets.erase(iter);
|
---|
| 440 | NotEmpty = false;
|
---|
| 441 | }
|
---|
| 442 | currenttargets.push_back(target);
|
---|
| 443 | if (elements.empty()) {
|
---|
| 444 | // call add function
|
---|
| 445 | {
|
---|
| 446 | std::stringstream targetstream;
|
---|
| 447 | BOOST_FOREACH( chargeiter_t target, currenttargets ) {
|
---|
| 448 | targetstream << " " << *target;
|
---|
| 449 | }
|
---|
| 450 | LOG(3, "DEBUG: Adding set" << targetstream.str() << ".");
|
---|
| 451 | }
|
---|
| 452 | addFunction(currenttargets);
|
---|
| 453 | } else {
|
---|
| 454 | // if not, call us recursively
|
---|
| 455 | pickLastElementAsTarget(elements, elementtargets, currenttargets, addFunction);
|
---|
| 456 | }
|
---|
| 457 | // pop last in currenset again
|
---|
| 458 | currenttargets.pop_back();
|
---|
| 459 | }
|
---|
| 460 | }
|
---|
| 461 |
|
---|
[691be4] | 462 | Extractors::chargeiters_t
|
---|
| 463 | Extractors::_detail::gatherTargetsFromFragment(
|
---|
| 464 | const Fragment::charges_t& charges,
|
---|
[c211f7] | 465 | const Fragment::charges_t elements
|
---|
[691be4] | 466 | )
|
---|
| 467 | {
|
---|
[c211f7] | 468 | /// The main problem here is that we have to know how many same
|
---|
| 469 | /// elements (but different atoms!) we are required to find. Hence,
|
---|
| 470 | /// we first have to count same elements, then get different targets
|
---|
| 471 | /// for each and then associated them in correct order back again.
|
---|
| 472 |
|
---|
| 473 | // 1. we have to make elements unique with counts, hence convert to map
|
---|
| 474 | elementcounts_t elementcounts =
|
---|
| 475 | Extractors::_detail::getElementCounts(elements);
|
---|
| 476 |
|
---|
| 477 | // 2. then for each element we need as many targets (chargeiters) as counts
|
---|
| 478 | elementtargets_t elementtargets =
|
---|
| 479 | Extractors::_detail::convertElementcountsToTargets(charges, elementcounts);
|
---|
[301dbf] | 480 |
|
---|
| 481 | // 3. we go again through elements and use one found target for each count
|
---|
| 482 | // in that order
|
---|
[63e786] | 483 | chargeiters_t targets =
|
---|
| 484 | Extractors::_detail::realignElementtargets(elementtargets, elements, elementcounts);
|
---|
| 485 |
|
---|
[301dbf] | 486 | #ifndef NDEBUG
|
---|
| 487 | // check all for debugging
|
---|
| 488 | for (chargeiters_t::const_iterator chargeiter = targets.begin();
|
---|
| 489 | chargeiter != targets.end();
|
---|
| 490 | ++chargeiter)
|
---|
| 491 | ASSERT( *chargeiter != charges.end(),
|
---|
[691be4] | 492 | "Extractors::gatherTargetsFromFragment() - we have not found enough targets?!");
|
---|
[301dbf] | 493 | #endif
|
---|
[691be4] | 494 |
|
---|
| 495 | return targets;
|
---|
| 496 | }
|
---|
| 497 |
|
---|
| 498 | Fragment::positions_t
|
---|
| 499 | Extractors::gatherPositionsFromFragment(
|
---|
| 500 | const Fragment::positions_t positions,
|
---|
| 501 | const Fragment::charges_t charges,
|
---|
| 502 | const Fragment::charges_t& elements
|
---|
| 503 | )
|
---|
| 504 | {
|
---|
| 505 | // 1.-3. gather correct charge positions
|
---|
| 506 | chargeiters_t targets =
|
---|
| 507 | Extractors::_detail::gatherTargetsFromFragment(charges, elements);
|
---|
[301dbf] | 508 | // 4. convert position_t to Vector
|
---|
[691be4] | 509 | return Extractors::_detail::gatherPositionsFromTargets(
|
---|
| 510 | positions,
|
---|
[301dbf] | 511 | charges,
|
---|
| 512 | targets);
|
---|
| 513 | }
|
---|
| 514 |
|
---|
[691be4] | 515 | FunctionModel::arguments_t
|
---|
| 516 | Extractors::gatherDistancesFromFragment(
|
---|
| 517 | const Fragment::positions_t positions,
|
---|
| 518 | const Fragment::charges_t charges,
|
---|
| 519 | const Fragment::charges_t& elements,
|
---|
| 520 | const size_t globalid
|
---|
| 521 | )
|
---|
| 522 | {
|
---|
| 523 | // 1.-3. gather correct charge positions
|
---|
| 524 | chargeiters_t targets =
|
---|
| 525 | Extractors::_detail::gatherTargetsFromFragment(charges, elements);
|
---|
| 526 | // 4. convert position_t to Vector
|
---|
| 527 | return Extractors::_detail::gatherDistancesFromTargets(
|
---|
| 528 | positions,
|
---|
| 529 | charges,
|
---|
| 530 | targets,
|
---|
| 531 | globalid);
|
---|
| 532 | }
|
---|
| 533 |
|
---|
[e1fe7e] | 534 | FunctionModel::list_of_arguments_t Extractors::reorderArgumentsByIncreasingDistance(
|
---|
| 535 | const FunctionModel::list_of_arguments_t &listargs
|
---|
[301dbf] | 536 | )
|
---|
| 537 | {
|
---|
[e1fe7e] | 538 | FunctionModel::list_of_arguments_t returnargs;
|
---|
| 539 | for (FunctionModel::list_of_arguments_t::const_iterator iter = listargs.begin();
|
---|
| 540 | iter != listargs.end(); ++iter) {
|
---|
| 541 | const FunctionModel::arguments_t &args = *iter;
|
---|
| 542 | FunctionModel::arguments_t sortedargs(args);
|
---|
| 543 | std::sort(sortedargs.begin(), sortedargs.end(), argument_t::DistanceComparator);
|
---|
| 544 | returnargs.push_back(sortedargs);
|
---|
| 545 | }
|
---|
[301dbf] | 546 | return returnargs;
|
---|
[8aa597] | 547 | }
|
---|
[301dbf] | 548 |
|
---|
[51e0e3] | 549 |
|
---|
| 550 | struct ParticleTypesComparator {
|
---|
| 551 | bool operator()(const argument_t::types_t &a, const argument_t::types_t &b)
|
---|
| 552 | {
|
---|
| 553 | if (a.first < a.second) {
|
---|
| 554 | if (b.first < b.second) {
|
---|
| 555 | if (a.first < b.first)
|
---|
| 556 | return true;
|
---|
| 557 | else if (a.first > b.first)
|
---|
| 558 | return false;
|
---|
| 559 | else
|
---|
| 560 | return (a.second < b.second);
|
---|
| 561 | } else {
|
---|
| 562 | if (a.first < b.second)
|
---|
| 563 | return true;
|
---|
| 564 | else if (a.first > b.second)
|
---|
| 565 | return false;
|
---|
| 566 | else
|
---|
| 567 | return (a.second < b.first);
|
---|
| 568 | }
|
---|
| 569 | } else {
|
---|
| 570 | if (b.first < b.second) {
|
---|
| 571 | if (a.second < b.first)
|
---|
| 572 | return true;
|
---|
| 573 | else if (a.second > b.first)
|
---|
| 574 | return false;
|
---|
| 575 | else
|
---|
| 576 | return (a.first < b.second);
|
---|
| 577 | } else {
|
---|
| 578 | if (a.second < b.second)
|
---|
| 579 | return true;
|
---|
| 580 | else if (a.second > b.second)
|
---|
| 581 | return false;
|
---|
| 582 | else
|
---|
| 583 | return (a.first < b.first);
|
---|
| 584 | }
|
---|
| 585 | }
|
---|
| 586 | }
|
---|
| 587 | };
|
---|
| 588 |
|
---|
| 589 | std::ostream& operator<<(std::ostream &out, const argument_t::types_t &a)
|
---|
| 590 | {
|
---|
| 591 | out << "[" << a.first << "," << a.second << "]";
|
---|
| 592 | return out;
|
---|
| 593 | }
|
---|
| 594 |
|
---|
[e1fe7e] | 595 | FunctionModel::list_of_arguments_t Extractors::reorderArgumentsByParticleTypes(
|
---|
| 596 | const FunctionModel::list_of_arguments_t &listargs,
|
---|
[df350c] | 597 | const ParticleTypes_t &_types
|
---|
| 598 | )
|
---|
[51e0e3] | 599 | {
|
---|
[e1fe7e] | 600 | FunctionModel::list_of_arguments_t returnargs;
|
---|
| 601 | for (FunctionModel::list_of_arguments_t::const_iterator iter = listargs.begin();
|
---|
| 602 | iter != listargs.end(); ++iter) {
|
---|
| 603 | const FunctionModel::arguments_t &args = *iter;
|
---|
| 604 | /// We place all arguments into multimap according to particle type pair.
|
---|
| 605 | // here, we need a special comparator such that types in key pair are always
|
---|
| 606 | // properly ordered.
|
---|
| 607 | typedef std::multimap<
|
---|
| 608 | argument_t::types_t,
|
---|
| 609 | argument_t,
|
---|
| 610 | ParticleTypesComparator> TypePair_Argument_Map_t;
|
---|
| 611 | TypePair_Argument_Map_t argument_map;
|
---|
| 612 | for(FunctionModel::arguments_t::const_iterator iter = args.begin();
|
---|
| 613 | iter != args.end(); ++iter) {
|
---|
| 614 | argument_map.insert( std::make_pair(iter->types, *iter) );
|
---|
| 615 | }
|
---|
| 616 | LOG(4, "DEBUG: particle_type map is " << argument_map << ".");
|
---|
[51e0e3] | 617 |
|
---|
[e1fe7e] | 618 | /// Then, we create the desired unique keys
|
---|
| 619 | typedef std::vector<argument_t::types_t> UniqueTypes_t;
|
---|
| 620 | UniqueTypes_t UniqueTypes;
|
---|
| 621 | for (ParticleTypes_t::const_iterator firstiter = _types.begin();
|
---|
| 622 | firstiter != _types.end();
|
---|
| 623 | ++firstiter) {
|
---|
| 624 | for (ParticleTypes_t::const_iterator seconditer = firstiter;
|
---|
| 625 | seconditer != _types.end();
|
---|
| 626 | ++seconditer) {
|
---|
| 627 | if (seconditer == firstiter)
|
---|
| 628 | continue;
|
---|
| 629 | UniqueTypes.push_back( std::make_pair(*firstiter, *seconditer) );
|
---|
| 630 | }
|
---|
[51e0e3] | 631 | }
|
---|
[e1fe7e] | 632 | LOG(4, "DEBUG: Created unique types as keys " << UniqueTypes << ".");
|
---|
| 633 |
|
---|
| 634 | /// Finally, we use the unique key list to pick corresponding arguments from the map
|
---|
| 635 | FunctionModel::arguments_t sortedargs;
|
---|
| 636 | sortedargs.reserve(args.size());
|
---|
| 637 | while (!argument_map.empty()) {
|
---|
| 638 | // note that particle_types_t may be flipped, i.e. 1,8 is equal to 8,1, but we
|
---|
| 639 | // must maintain the correct order in indices in accordance with the order
|
---|
| 640 | // in _types, i.e. 1,8,1 must match with e.g. ids 1,0,2 where 1 has type 1,
|
---|
| 641 | // 0 has type 8, and 2 has type 2.
|
---|
| 642 | // In other words: We do not want to flip/modify arguments such that they match
|
---|
| 643 | // with the specific type pair we seek but then this comes at the price that we
|
---|
| 644 | // have flip indices when the types in a pair are flipped.
|
---|
| 645 |
|
---|
| 646 | typedef std::vector<size_t> indices_t;
|
---|
| 647 | //!> here, we gather the indices as we discover them
|
---|
| 648 | indices_t indices;
|
---|
| 649 | indices.resize(_types.size(), (size_t)-1);
|
---|
| 650 |
|
---|
| 651 | // these are two iterators that create index pairs in the same way as we have
|
---|
| 652 | // created type pairs. If a -1 is still present in indices, then the index is
|
---|
| 653 | // still arbitrary but is then set by the next found index
|
---|
| 654 | indices_t::iterator firstindex = indices.begin();
|
---|
| 655 | indices_t::iterator secondindex = firstindex+1;
|
---|
| 656 |
|
---|
| 657 | //!> here, we gather the current bunch of arguments as we find them
|
---|
| 658 | FunctionModel::arguments_t argumentbunch;
|
---|
| 659 | argumentbunch.reserve(UniqueTypes.size());
|
---|
| 660 |
|
---|
| 661 | for (UniqueTypes_t::const_iterator typeiter = UniqueTypes.begin();
|
---|
| 662 | typeiter != UniqueTypes.end(); ++typeiter) {
|
---|
| 663 | // have all arguments to same type pair as list within the found range
|
---|
| 664 | std::pair<
|
---|
| 665 | TypePair_Argument_Map_t::iterator,
|
---|
| 666 | TypePair_Argument_Map_t::iterator> range_t =
|
---|
| 667 | argument_map.equal_range(*typeiter);
|
---|
| 668 | LOG(4, "DEBUG: Set of arguments to current key [" << typeiter->first << ","
|
---|
| 669 | << typeiter->second << "] is " << std::list<argument_t>(
|
---|
| 670 | MapValueIterator<TypePair_Argument_Map_t::iterator>(range_t.first),
|
---|
| 671 | MapValueIterator<TypePair_Argument_Map_t::iterator>(range_t.second)
|
---|
| 672 | ) << ".");
|
---|
| 673 | // the first key is always easy and is pivot which the rest has to be associated to
|
---|
| 674 | if (typeiter == UniqueTypes.begin()) {
|
---|
| 675 | const argument_t & arg = range_t.first->second;
|
---|
| 676 | if ((typeiter->first == arg.types.first) && (typeiter->second == arg.types.second)) {
|
---|
| 677 | // store in correct order
|
---|
| 678 | *firstindex = arg.indices.first;
|
---|
| 679 | *secondindex = arg.indices.second;
|
---|
| 680 | } else {
|
---|
| 681 | // store in flipped order
|
---|
| 682 | *firstindex = arg.indices.second;
|
---|
| 683 | *secondindex = arg.indices.first;
|
---|
| 684 | }
|
---|
| 685 | argumentbunch.push_back(arg);
|
---|
| 686 | argument_map.erase(range_t.first);
|
---|
| 687 | LOG(4, "DEBUG: Gathered first argument " << arg << ".");
|
---|
[51e0e3] | 688 | } else {
|
---|
[e1fe7e] | 689 | // go through the range and pick the first argument matching the index constraints
|
---|
| 690 | for (TypePair_Argument_Map_t::iterator argiter = range_t.first;
|
---|
| 691 | argiter != range_t.second; ++argiter) {
|
---|
| 692 | // seconditer may be -1 still
|
---|
| 693 | const argument_t &arg = argiter->second;
|
---|
| 694 | if (arg.indices.first == *firstindex) {
|
---|
| 695 | if ((arg.indices.second == *secondindex) || (*secondindex == (size_t)-1)) {
|
---|
| 696 | if (*secondindex == (size_t)-1)
|
---|
| 697 | *secondindex = arg.indices.second;
|
---|
| 698 | argumentbunch.push_back(arg);
|
---|
| 699 | argument_map.erase(argiter);
|
---|
| 700 | LOG(4, "DEBUG: Gathered another argument " << arg << ".");
|
---|
| 701 | break;
|
---|
| 702 | }
|
---|
| 703 | } else if ((arg.indices.first == *secondindex) || (*secondindex == (size_t)-1)) {
|
---|
| 704 | if (arg.indices.second == *firstindex) {
|
---|
| 705 | if (*secondindex == (size_t)-1)
|
---|
| 706 | *secondindex = arg.indices.first;
|
---|
| 707 | argumentbunch.push_back(arg);
|
---|
| 708 | argument_map.erase(argiter);
|
---|
| 709 | LOG(4, "DEBUG: Gathered another (flipped) argument " << arg << ".");
|
---|
| 710 | break;
|
---|
| 711 | }
|
---|
[51e0e3] | 712 | }
|
---|
| 713 | }
|
---|
| 714 | }
|
---|
[e1fe7e] | 715 | // move along in indices and check bounds
|
---|
| 716 | ++secondindex;
|
---|
| 717 | if (secondindex == indices.end()) {
|
---|
| 718 | ++firstindex;
|
---|
| 719 | if (firstindex != indices.end()-1)
|
---|
| 720 | secondindex = firstindex+1;
|
---|
| 721 | }
|
---|
[51e0e3] | 722 | }
|
---|
[e1fe7e] | 723 | ASSERT( (firstindex == indices.end()-1) && (secondindex == indices.end()),
|
---|
| 724 | "Extractors::reorderArgumentsByParticleTypes() - we have not gathered enough arguments.");
|
---|
| 725 | ASSERT( argumentbunch.size() == UniqueTypes.size(),
|
---|
| 726 | "Extractors::reorderArgumentsByParticleTypes() - we have not gathered enough arguments.");
|
---|
| 727 | // place bunch of arguments in return args
|
---|
| 728 | LOG(3, "DEBUG: Given types " << _types << " and found indices " << indices << ".");
|
---|
| 729 | LOG(3, "DEBUG: Final bunch of arguments is " << argumentbunch << ".");
|
---|
| 730 | sortedargs.insert(sortedargs.end(), argumentbunch.begin(), argumentbunch.end());
|
---|
[51e0e3] | 731 | }
|
---|
[e1fe7e] | 732 | returnargs.push_back(sortedargs);
|
---|
[51e0e3] | 733 | }
|
---|
| 734 |
|
---|
| 735 | return returnargs;
|
---|
| 736 | }
|
---|
| 737 |
|
---|
[e1fe7e] | 738 | FunctionModel::list_of_arguments_t Extractors::filterArgumentsByParticleTypes(
|
---|
[51e0e3] | 739 | const FunctionModel::arguments_t &args,
|
---|
| 740 | const ParticleTypes_t &_types
|
---|
| 741 | )
|
---|
[df350c] | 742 | {
|
---|
| 743 | typedef std::list< argument_t > ListArguments_t;
|
---|
| 744 | ListArguments_t availableList(args.begin(), args.end());
|
---|
[31a2be] | 745 | LOG(2, "DEBUG: Initial list of args is " << args << ".");
|
---|
| 746 |
|
---|
[df350c] | 747 |
|
---|
| 748 | // TODO: fill a lookup map such that we don't have O(M^3) scaling, if M is number
|
---|
| 749 | // of types (and we always must have M(M-1)/2 args) but O(M^2 log(M)). However, as
|
---|
| 750 | // M is very small (<=3), this is not necessary fruitful now.
|
---|
| 751 | // typedef ParticleTypes_t firsttype;
|
---|
| 752 | // typedef ParticleTypes_t secondtype;
|
---|
| 753 | // typedef std::map< firsttype, std::map< secondtype, boost::ref(args) > > ArgsLookup_t;
|
---|
| 754 | // ArgsLookup_t ArgsLookup;
|
---|
| 755 |
|
---|
| 756 | // basically, we have two choose any two pairs out of types but only those
|
---|
[51e0e3] | 757 | // where the first is less than the latter. Hence, we start the second
|
---|
[df350c] | 758 | // iterator at the current position of the first one and skip the equal case.
|
---|
[e1fe7e] | 759 | FunctionModel::arguments_t allargs;
|
---|
| 760 | allargs.reserve(args.size());
|
---|
[df350c] | 761 | for (ParticleTypes_t::const_iterator firstiter = _types.begin();
|
---|
| 762 | firstiter != _types.end();
|
---|
| 763 | ++firstiter) {
|
---|
| 764 | for (ParticleTypes_t::const_iterator seconditer = firstiter;
|
---|
| 765 | seconditer != _types.end();
|
---|
| 766 | ++seconditer) {
|
---|
| 767 | if (seconditer == firstiter)
|
---|
| 768 | continue;
|
---|
[e1fe7e] | 769 | LOG(3, "DEBUG: Looking for (" << *firstiter << "," << *seconditer << ") in all args.");
|
---|
[df350c] | 770 |
|
---|
| 771 | // search the right one in _args (we might allow switching places of
|
---|
| 772 | // firstiter and seconditer, as distance is symmetric).
|
---|
| 773 | ListArguments_t::iterator iter = availableList.begin();
|
---|
[31a2be] | 774 | while (iter != availableList.end()) {
|
---|
[e1fe7e] | 775 | LOG(4, "DEBUG: Current args is " << *iter << ".");
|
---|
[df350c] | 776 | if ((iter->types.first == *firstiter)
|
---|
| 777 | && (iter->types.second == *seconditer)) {
|
---|
[e1fe7e] | 778 | allargs.push_back( *iter );
|
---|
[31a2be] | 779 | iter = availableList.erase(iter);
|
---|
| 780 | LOG(4, "DEBUG: Accepted argument.");
|
---|
| 781 | } else if ((iter->types.first == *seconditer)
|
---|
[df350c] | 782 | && (iter->types.second == *firstiter)) {
|
---|
[e1fe7e] | 783 | allargs.push_back( *iter );
|
---|
[51e0e3] | 784 | iter = availableList.erase(iter);
|
---|
| 785 | LOG(4, "DEBUG: Accepted (flipped) argument.");
|
---|
| 786 | } else {
|
---|
| 787 | ++iter;
|
---|
| 788 | LOG(4, "DEBUG: Rejected argument.");
|
---|
[df350c] | 789 | }
|
---|
| 790 | }
|
---|
| 791 | }
|
---|
| 792 | }
|
---|
[e1fe7e] | 793 | LOG(2, "DEBUG: Final list of args is " << allargs << ".");
|
---|
| 794 |
|
---|
| 795 | // first, we bring together tuples of distances that belong together
|
---|
| 796 | FunctionModel::list_of_arguments_t singlelist_allargs;
|
---|
| 797 | singlelist_allargs.push_back(allargs);
|
---|
| 798 | FunctionModel::list_of_arguments_t sortedargs =
|
---|
| 799 | reorderArgumentsByParticleTypes(singlelist_allargs, _types);
|
---|
| 800 | ASSERT( sortedargs.size() == (size_t)1,
|
---|
| 801 | "Extractors::filterArgumentsByParticleTypes() - reordering did not generate a single list.");
|
---|
| 802 | // then we split up the tuples of arguments and place each into single list
|
---|
| 803 | FunctionModel::list_of_arguments_t returnargs;
|
---|
| 804 | FunctionModel::arguments_t::const_iterator argiter = sortedargs.begin()->begin();
|
---|
| 805 | const size_t num_types = _types.size();
|
---|
| 806 | const size_t args_per_tuple = num_types * (num_types-1) / 2;
|
---|
| 807 | while (argiter != sortedargs.begin()->end()) {
|
---|
| 808 | FunctionModel::arguments_t currenttuple(args_per_tuple);
|
---|
| 809 | const FunctionModel::arguments_t::const_iterator startiter = argiter;
|
---|
| 810 | std::advance(argiter, args_per_tuple);
|
---|
| 811 | #ifndef NDEBUG
|
---|
| 812 | FunctionModel::arguments_t::const_iterator endoutiter =
|
---|
| 813 | #endif
|
---|
| 814 | std::copy(startiter, argiter, currenttuple.begin());
|
---|
| 815 | ASSERT( endoutiter == currenttuple.end(),
|
---|
| 816 | "Extractors::filterArgumentsByParticleTypes() - currenttuple not initialized to right size.");
|
---|
| 817 | returnargs.push_back(currenttuple);
|
---|
| 818 | }
|
---|
| 819 |
|
---|
| 820 | LOG(2, "DEBUG: We have generated " << returnargs.size() << " tuples of distances.");
|
---|
[df350c] | 821 |
|
---|
| 822 | return returnargs;
|
---|
| 823 | }
|
---|
[9897ee9] | 824 |
|
---|
| 825 |
|
---|
| 826 | FunctionModel::arguments_t Extractors::combineArguments(
|
---|
| 827 | const FunctionModel::arguments_t &firstargs,
|
---|
| 828 | const FunctionModel::arguments_t &secondargs)
|
---|
| 829 | {
|
---|
[cf4905] | 830 | FunctionModel::arguments_t args = concatenateArguments(firstargs, secondargs);
|
---|
[64bdfd] | 831 | std::sort(args.begin(), args.end(),
|
---|
| 832 | boost::bind(&argument_t::operator<, _1, _2));
|
---|
| 833 | FunctionModel::arguments_t::iterator iter =
|
---|
| 834 | std::unique(args.begin(), args.end(),
|
---|
| 835 | boost::bind(&argument_t::operator==, _1, _2));
|
---|
| 836 | args.erase(iter, args.end());
|
---|
[9897ee9] | 837 | return args;
|
---|
| 838 | }
|
---|
[64bdfd] | 839 |
|
---|
[cf4905] | 840 | FunctionModel::arguments_t Extractors::concatenateArguments(
|
---|
| 841 | const FunctionModel::arguments_t &firstargs,
|
---|
| 842 | const FunctionModel::arguments_t &secondargs)
|
---|
| 843 | {
|
---|
| 844 | FunctionModel::arguments_t args(firstargs);
|
---|
| 845 | args.insert(args.end(), secondargs.begin(), secondargs.end());
|
---|
| 846 | return args;
|
---|
| 847 | }
|
---|
| 848 |
|
---|
[e1fe7e] | 849 | FunctionModel::list_of_arguments_t Extractors::concatenateListOfArguments(
|
---|
| 850 | const FunctionModel::list_of_arguments_t &firstlistargs,
|
---|
| 851 | const FunctionModel::list_of_arguments_t &secondlistargs)
|
---|
| 852 | {
|
---|
| 853 | FunctionModel::list_of_arguments_t listargs(firstlistargs);
|
---|
| 854 | listargs.insert(listargs.end(), secondlistargs.begin(), secondlistargs.end());
|
---|
| 855 | return listargs;
|
---|
| 856 | }
|
---|