[bcf653] | 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 University of Bonn. All rights reserved.
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| 5 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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| 6 | */
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| 7 |
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[d02e07] | 8 | /*
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| 9 | * SurfaceCorrelationAction.cpp
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| 10 | *
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| 11 | * Created on: May 9, 2010
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| 12 | * Author: heber
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| 13 | */
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| 14 |
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[bf3817] | 15 | // include config.h
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| 16 | #ifdef HAVE_CONFIG_H
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| 17 | #include <config.h>
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| 18 | #endif
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| 19 |
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[ad011c] | 20 | #include "CodePatterns/MemDebug.hpp"
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[d02e07] | 21 |
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| 22 | #include "analysis_correlation.hpp"
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| 23 | #include "boundary.hpp"
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| 24 | #include "linkedcell.hpp"
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[ad011c] | 25 | #include "CodePatterns/Verbose.hpp"
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| 26 | #include "CodePatterns/Log.hpp"
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[d02e07] | 27 | #include "element.hpp"
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| 28 | #include "molecule.hpp"
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| 29 | #include "periodentafel.hpp"
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[88b400] | 30 | #include "tesselation.hpp"
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[57f243] | 31 | #include "LinearAlgebra/Vector.hpp"
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[d02e07] | 32 | #include "World.hpp"
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| 33 |
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| 34 | #include <iostream>
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| 35 | #include <string>
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| 36 |
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| 37 | using namespace std;
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| 38 |
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[9ee38b] | 39 | #include "Actions/AnalysisAction/SurfaceCorrelationAction.hpp"
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[d02e07] | 40 |
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[9ee38b] | 41 | // and construct the stuff
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| 42 | #include "SurfaceCorrelationAction.def"
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| 43 | #include "Action_impl_pre.hpp"
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[d02e07] | 44 |
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[9ee38b] | 45 | /** =========== define the function ====================== */
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[d02e07] | 46 | Action::state_ptr AnalysisSurfaceCorrelationAction::performCall() {
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| 47 | int ranges[3] = {1, 1, 1};
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| 48 | ofstream output;
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| 49 | ofstream binoutput;
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| 50 | string type;
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| 51 | BinPairMap *binmap = NULL;
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| 52 |
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| 53 | // obtain information
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[9ee38b] | 54 | getParametersfromValueStorage();
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[d02e07] | 55 |
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| 56 | // execute action
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[e4afb4] | 57 | output.open(params.outputname.string().c_str());
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| 58 | binoutput.open(params.binoutputname.string().c_str());
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[9ee38b] | 59 | ASSERT(params.Boundary != NULL, "No molecule specified for SurfaceCorrelation.");
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[d02e07] | 60 | const double radius = 4.;
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| 61 | double LCWidth = 20.;
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[9ee38b] | 62 | if (params.BinEnd > 0) {
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| 63 | if (params.BinEnd > 2.*radius)
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| 64 | LCWidth = params.BinEnd;
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[d02e07] | 65 | else
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| 66 | LCWidth = 2.*radius;
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| 67 | }
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| 68 |
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| 69 | // get the boundary
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| 70 | class Tesselation *TesselStruct = NULL;
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| 71 | const LinkedCell *LCList = NULL;
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| 72 | // find biggest molecule
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[e65de8] | 73 | std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
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[faa1c9] | 74 | std::cout << "There are " << molecules.size() << " selected molecules." << std::endl;
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[af2c424] | 75 | LCList = new LinkedCell(*params.Boundary, LCWidth);
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[9ee38b] | 76 | FindNonConvexBorder(params.Boundary, TesselStruct, LCList, radius, NULL);
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[d02e07] | 77 | CorrelationToSurfaceMap *surfacemap = NULL;
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[9ee38b] | 78 | if (params.periodic)
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| 79 | surfacemap = PeriodicCorrelationToSurface( molecules, params.elements, TesselStruct, LCList, ranges);
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[d02e07] | 80 | else
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[9ee38b] | 81 | surfacemap = CorrelationToSurface( molecules, params.elements, TesselStruct, LCList);
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[d02e07] | 82 | delete LCList;
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[92e5cb] | 83 | OutputCorrelationMap<CorrelationToSurfaceMap>(&output, surfacemap, OutputCorrelationToSurface_Header, OutputCorrelationToSurface_Value);
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[d02e07] | 84 | // check whether radius was appropriate
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| 85 | {
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| 86 | double start; double end;
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| 87 | GetMinMax( surfacemap, start, end);
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| 88 | if (LCWidth < end)
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| 89 | DoeLog(1) && (eLog()<< Verbose(1) << "Linked Cell width is smaller than the found range of values! Bins can only be correct up to: " << radius << "." << endl);
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| 90 | }
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[9ee38b] | 91 | binmap = BinData( surfacemap, params.BinWidth, params.BinStart, params.BinEnd );
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[92e5cb] | 92 | OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
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[d02e07] | 93 | delete TesselStruct; // surfacemap contains refs to triangles! delete here, not earlier!
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| 94 | delete(binmap);
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| 95 | delete(surfacemap);
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| 96 | output.close();
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| 97 | binoutput.close();
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| 98 | return Action::success;
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| 99 | }
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| 100 |
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| 101 | Action::state_ptr AnalysisSurfaceCorrelationAction::performUndo(Action::state_ptr _state) {
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| 102 | return Action::success;
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| 103 | }
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| 104 |
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| 105 | Action::state_ptr AnalysisSurfaceCorrelationAction::performRedo(Action::state_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 | bool AnalysisSurfaceCorrelationAction::canUndo() {
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| 110 | return true;
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| 111 | }
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| 112 |
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| 113 | bool AnalysisSurfaceCorrelationAction::shouldUndo() {
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| 114 | return true;
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| 115 | }
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[9ee38b] | 116 | /** =========== end of function ====================== */
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