1 | /*
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2 | * Project: MoleCuilder
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3 | * Description: creates and alters molecular systems
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4 | * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
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5 | *
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6 | *
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7 | * This file is part of MoleCuilder.
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8 | *
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9 | * MoleCuilder is free software: you can redistribute it and/or modify
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10 | * it under the terms of the GNU General Public License as published by
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11 | * the Free Software Foundation, either version 2 of the License, or
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12 | * (at your option) any later version.
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13 | *
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14 | * MoleCuilder is distributed in the hope that it will be useful,
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15 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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16 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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17 | * GNU General Public License for more details.
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18 | *
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19 | * You should have received a copy of the GNU General Public License
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20 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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21 | */
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22 |
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23 | /*
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24 | * DipoleAngularCorrelationAction.cpp
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25 | *
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26 | * Created on: Feb 11, 2011
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27 | * Author: heber
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28 | */
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29 |
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30 | // include config.h
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31 | #ifdef HAVE_CONFIG_H
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32 | #include <config.h>
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33 | #endif
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34 |
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35 | //#include "CodePatterns/MemDebug.hpp"
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36 |
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37 | #include "Analysis/analysis_correlation.hpp"
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38 | #include "CodePatterns/Log.hpp"
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39 | #include "Descriptors/AtomOfMoleculeSelectionDescriptor.hpp"
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40 | #include "Descriptors/MoleculeFormulaDescriptor.hpp"
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41 | #include "Element/element.hpp"
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42 | #include "Element/periodentafel.hpp"
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43 | #include "LinearAlgebra/Vector.hpp"
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44 | #include "molecule.hpp"
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45 | #include "World.hpp"
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46 | #include "WorldTime.hpp"
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47 |
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48 | #include <iostream>
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49 | #include <map>
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50 | #include <string>
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51 |
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52 | #include "Actions/AnalysisAction/DipoleAngularCorrelationAction.hpp"
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53 |
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54 | using namespace MoleCuilder;
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55 |
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56 | // and construct the stuff
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57 | #include "DipoleAngularCorrelationAction.def"
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58 | #include "Action_impl_pre.hpp"
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59 |
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60 | /** =========== define the function ====================== */
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61 | ActionState::ptr AnalysisDipoleAngularCorrelationAction::performCall() {
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62 | //int ranges[3] = {1, 1, 1};
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63 | string type;
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64 |
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65 | // get selected atoms
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66 | std::vector<const atom*> old_atom_selection =
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67 | const_cast<const World &>(World::getInstance()).getSelectedAtoms();
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68 | std::vector<const molecule*> old_molecule_selection =
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69 | const_cast<const World &>(World::getInstance()).getSelectedMolecules();
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70 |
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71 | // get current time step
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72 | const unsigned int oldtime = WorldTime::getTime();
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73 |
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74 | // select atoms and obtain zero dipole orientation
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75 | Formula DipoleFormula(params.DipoleFormula.get());
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76 | World::getInstance().setTime(params.timestepzero.get());
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77 | World::getInstance().clearMoleculeSelection(); // TODO: This should be done in setTime or where molecules are re-done
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78 | World::getInstance().selectAllMolecules(MoleculeByFormula(DipoleFormula));
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79 | std::vector<const molecule *> molecules =
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80 | const_cast<const World &>(World::getInstance()).getSelectedMolecules();
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81 | std::map<atomId_t, Vector> ZeroVector = CalculateZeroAngularDipole(molecules);
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82 |
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83 | // go through each step of common trajectory of all atoms in set
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84 | World::getInstance().clearAtomSelection();
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85 | World::getInstance().selectAllAtoms(AtomsByMoleculeSelection());
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86 | std::vector<const atom *> atoms = const_cast<const World &>(World::getInstance()).
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87 | getSelectedAtoms();
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88 | if (atoms.empty()) {
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89 | STATUS("Formula "+toString(DipoleFormula)+" selects no atoms.");
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90 | return Action::failure;
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91 | }
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92 | range<size_t> timesteps = getMaximumTrajectoryBounds(atoms);
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93 | ASSERT(params.timestepzero.get() < timesteps.first,
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94 | "AnalysisDipoleAngularCorrelationAction::performCall() - time step zero "
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95 | +toString(params.timestepzero.get())+" is beyond trajectory range ("
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96 | +toString(timesteps.first)+") of some atoms.");
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97 | for (size_t step = params.timestepzero.get(); step < timesteps.first; ++step) {
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98 | // calculate dipoles relative to zero orientation
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99 | DipoleAngularCorrelationMap *correlationmap = NULL;
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100 | correlationmap = DipoleAngularCorrelation(DipoleFormula, step, ZeroVector, DontResetTime);
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101 |
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102 | // prepare step string in filename
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103 | std::stringstream stepstream;
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104 | stepstream << std::setw(4) << std::setfill('0') << step;
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105 | const std::string stepname(stepstream.str());
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106 |
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107 | // output correlation map
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108 | ofstream output;
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109 | std::string filename = params.outputname.get().string()+"."+stepname+".dat";
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110 | output.open(filename.c_str());
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111 | OutputCorrelationMap<DipoleAngularCorrelationMap>(&output, correlationmap, OutputDipoleAngularCorrelation_Header, OutputDipoleAngularCorrelation_Value);
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112 | output.close();
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113 |
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114 | // bin map
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115 | BinPairMap *binmap = BinData( correlationmap, params.BinWidth.get(), params.BinStart.get(), params.BinEnd.get() );
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116 |
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117 | // free correlation map
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118 | delete correlationmap;
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119 |
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120 | // output binned map
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121 | ofstream binoutput;
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122 | std::string binfilename = params.binoutputname.get().string()+"."+stepname+".dat";
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123 | binoutput.open(binfilename.c_str());
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124 | OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
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125 | binoutput.close();
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126 |
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127 | // free binned map
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128 | delete binmap;
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129 | }
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130 |
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131 | // reset to old time step
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132 | World::getInstance().setTime(oldtime);
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133 |
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134 | // reset to old selections
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135 | World::getInstance().clearAtomSelection();
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136 | BOOST_FOREACH(const atom *_atom, old_atom_selection) {
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137 | World::getInstance().selectAtom(_atom);
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138 | }
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139 | World::getInstance().clearMoleculeSelection();
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140 | BOOST_FOREACH(const molecule *_mol, old_molecule_selection) {
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141 | World::getInstance().selectMolecule(_mol);
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142 | }
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143 |
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144 | // exit
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145 | STATUS("Dipole angular correlation calculation successful.");
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146 | return Action::success;
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147 | }
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148 |
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149 | ActionState::ptr AnalysisDipoleAngularCorrelationAction::performUndo(ActionState::ptr _state) {
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150 | return Action::success;
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151 | }
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152 |
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153 | ActionState::ptr AnalysisDipoleAngularCorrelationAction::performRedo(ActionState::ptr _state){
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154 | return Action::success;
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155 | }
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156 |
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157 | bool AnalysisDipoleAngularCorrelationAction::canUndo() {
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158 | return true;
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159 | }
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160 |
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161 | bool AnalysisDipoleAngularCorrelationAction::shouldUndo() {
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162 | return true;
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163 | }
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164 | /** =========== end of function ====================== */
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