| 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 | * PairCorrelationAction.cpp
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| 25 | *
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| 26 | * Created on: May 9, 2010
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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/Verbose.hpp"
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| 39 | #include "CodePatterns/Log.hpp"
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| 40 | #include "Descriptors/AtomTypeDescriptor.hpp"
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| 41 | #include "Element/element.hpp"
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| 42 | #include "molecule.hpp"
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| 43 | #include "Element/periodentafel.hpp"
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| 44 | #include "LinearAlgebra/RealSpaceMatrix.hpp"
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| 45 | #include "LinearAlgebra/Vector.hpp"
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| 46 | #include "World.hpp"
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| 47 |
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| 48 | #include <iostream>
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| 49 | #include <string>
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| 50 |
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| 51 | #include "Actions/AnalysisAction/PairCorrelationAction.hpp"
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| 52 |
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| 53 | using namespace MoleCuilder;
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| 54 |
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| 55 | // and construct the stuff
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| 56 | #include "PairCorrelationAction.def"
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| 57 | #include "Action_impl_pre.hpp"
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| 58 |
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| 59 | /** =========== define the function ====================== */
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| 60 | ActionState::ptr AnalysisPairCorrelationAction::performCall() {
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| 61 | ofstream output;
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| 62 | ofstream binoutput;
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| 63 | string type;
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| 64 | BinPairMap *binmap = NULL;
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| 65 |
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| 66 | // execute action
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| 67 | output.open(params.outputname.get().string().c_str());
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| 68 | binoutput.open(params.binoutputname.get().string().c_str());
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| 69 | PairCorrelationMap *correlationmap = NULL;
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| 70 | World::ConstAtomComposite atoms_first;
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| 71 | World::ConstAtomComposite atoms_second;
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| 72 | if (params.elements.get().size() == 2) {
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| 73 | std::vector<const element *>::const_iterator elemiter = params.elements.get().begin();
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| 74 | atoms_first = World::getConstInstance().getAllAtoms(AtomByType(*(elemiter++)));
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| 75 | if (elemiter != params.elements.get().end()) {
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| 76 | atoms_second = World::getConstInstance().getAllAtoms(AtomByType(*(elemiter++)));
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| 77 | } else {
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| 78 | atoms_second = World::getConstInstance().getSelectedAtoms();
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| 79 | }
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| 80 | } else if (params.elements.get().size() == 1) {
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| 81 | std::vector<const element *>::const_iterator elemiter = params.elements.get().begin();
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| 82 | atoms_first = World::getConstInstance().getSelectedAtoms();
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| 83 | atoms_second = World::getConstInstance().getAllAtoms(AtomByType(*(elemiter++)));
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| 84 | } else {
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| 85 | STATUS("Either one or two elements must be given.");
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| 86 | return Action::failure;
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| 87 | }
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| 88 | double max_distance = params.BinEnd.get();
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| 89 | if (params.BinEnd.get() <= 0.) {
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| 90 | // find max distance within box from diagonal
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| 91 | const RealSpaceMatrix &M = World::getInstance().getDomain().getM();
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| 92 | max_distance = (M * Vector(1.,1.,1.)).NormSquared();
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| 93 | }
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| 94 | correlationmap = PairCorrelation(atoms_first, atoms_second, max_distance);
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| 95 | OutputCorrelationMap<PairCorrelationMap>(&output, correlationmap, OutputPairCorrelation_Header, OutputPairCorrelation_Value);
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| 96 | binmap = BinData( correlationmap, params.BinWidth.get(), params.BinStart.get(), params.BinEnd.get() );
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| 97 | OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
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| 98 | delete binmap;
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| 99 | delete correlationmap;
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| 100 | output.close();
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| 101 | binoutput.close();
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| 102 | return Action::success;
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| 103 | }
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| 104 |
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| 105 | ActionState::ptr AnalysisPairCorrelationAction::performUndo(ActionState::ptr _state) {
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| 106 | return Action::success;
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| 107 | }
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| 108 |
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| 109 | ActionState::ptr AnalysisPairCorrelationAction::performRedo(ActionState::ptr _state){
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| 110 | return Action::success;
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| 111 | }
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| 112 |
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| 113 | bool AnalysisPairCorrelationAction::canUndo() {
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| 114 | return true;
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| 115 | }
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| 116 |
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| 117 | bool AnalysisPairCorrelationAction::shouldUndo() {
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| 118 | return true;
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| 119 | }
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| 120 | /** =========== end of function ====================== */
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