source: src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

Candidate_v1.6.1
Last change on this file was 9eb71b3, checked in by Frederik Heber <frederik.heber@…>, 8 years ago

Commented out MemDebug include and Memory::ignore.

  • MemDebug clashes with various allocation operators that use a specific placement in memory. It is so far not possible to wrap new/delete fully. Hence, we stop this effort which so far has forced us to put ever more includes (with clashes) into MemDebug and thereby bloat compilation time.
  • MemDebug does not add that much usefulness which is not also provided by valgrind.
  • Property mode set to 100644
File size: 4.6 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
5 *
6 *
7 * This file is part of MoleCuilder.
8 *
9 * MoleCuilder is free software: you can redistribute it and/or modify
10 * it under the terms of the GNU General Public License as published by
11 * the Free Software Foundation, either version 2 of the License, or
12 * (at your option) any later version.
13 *
14 * MoleCuilder is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 * GNU General Public License for more details.
18 *
19 * You should have received a copy of the GNU General Public License
20 * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
21 */
22
23/*
24 * SurfaceCorrelationAction.cpp
25 *
26 * Created on: May 9, 2010
27 * Author: heber
28 */
29
30// include config.h
31#ifdef HAVE_CONFIG_H
32#include <config.h>
33#endif
34
35//#include "CodePatterns/MemDebug.hpp"
36
37#include "Analysis/analysis_correlation.hpp"
38#include "CodePatterns/Log.hpp"
39#include "Descriptors/MoleculeIdDescriptor.hpp"
40#include "Element/element.hpp"
41#include "Element/periodentafel.hpp"
42#include "LinearAlgebra/Vector.hpp"
43#include "LinkedCell/linkedcell.hpp"
44#include "LinkedCell/PointCloudAdaptor.hpp"
45#include "molecule.hpp"
46#include "Tesselation/boundary.hpp"
47#include "Tesselation/tesselation.hpp"
48#include "World.hpp"
49
50#include <iostream>
51#include <string>
52
53#include "Actions/AnalysisAction/SurfaceCorrelationAction.hpp"
54
55using namespace MoleCuilder;
56
57// and construct the stuff
58#include "SurfaceCorrelationAction.def"
59#include "Action_impl_pre.hpp"
60
61/** =========== define the function ====================== */
62ActionState::ptr AnalysisSurfaceCorrelationAction::performCall() {
63 int ranges[3] = {1, 1, 1};
64 ofstream output;
65 ofstream binoutput;
66 string type;
67 BinPairMap *binmap = NULL;
68
69 // execute action
70 output.open(params.outputname.get().string().c_str());
71 binoutput.open(params.binoutputname.get().string().c_str());
72
73 // check for selected molecules and create surfaces from them
74 std::vector<atom *> atoms(World::getInstance().getSelectedAtoms());
75 LinkedCell_deprecated * LCList = NULL;
76 Tesselation * TesselStruct = NULL;
77 const double radius = 4.;
78 double LCWidth = 20.;
79 if (params.BinEnd.get() > 0) {
80 if (params.BinEnd.get() > 2.*radius)
81 LCWidth = params.BinEnd.get();
82 else
83 LCWidth = 2.*radius;
84 }
85 if ( atoms.size() == 0) {
86 STATUS("You have not select any atoms.");
87 return Action::failure;
88 }
89 // create adaptor for the selected atoms
90 PointCloudAdaptor< std::vector<atom *> > cloud(&atoms, std::string("Selected atoms"));
91
92 // create tesselation
93 LCList = new LinkedCell_deprecated(cloud, 2.*radius);
94 TesselStruct = new Tesselation;
95 (*TesselStruct)(cloud, radius);
96
97 // correlate
98 const std::vector<const molecule*> molecules =
99 const_cast<const World &>(World::getInstance()).getSelectedMolecules();
100 std::cout << "There are " << molecules.size() << " selected molecules." << std::endl;
101 CorrelationToSurfaceMap *surfacemap = NULL;
102 if (params.periodic.get())
103 surfacemap = PeriodicCorrelationToSurface( molecules, params.elements.get(), TesselStruct, LCList, ranges);
104 else
105 surfacemap = CorrelationToSurface( molecules, params.elements.get(), TesselStruct, LCList);
106 delete LCList;
107 OutputCorrelationMap<CorrelationToSurfaceMap>(&output, surfacemap, OutputCorrelationToSurface_Header, OutputCorrelationToSurface_Value);
108 // check whether radius was appropriate
109 {
110 double start; double end;
111 GetMinMax( surfacemap, start, end);
112 if (LCWidth < end)
113 ELOG(1, "Linked Cell width is smaller than the found range of values! Bins can only be correct up to: " << radius << ".");
114 }
115 binmap = BinData( surfacemap, params.BinWidth.get(), params.BinStart.get(), params.BinEnd.get() );
116 OutputCorrelationMap<BinPairMap> ( &binoutput, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
117 delete TesselStruct; // surfacemap contains refs to triangles! delete here, not earlier!
118 delete binmap;
119 delete surfacemap;
120 output.close();
121 binoutput.close();
122 return Action::success;
123}
124
125ActionState::ptr AnalysisSurfaceCorrelationAction::performUndo(ActionState::ptr _state) {
126 return Action::success;
127}
128
129ActionState::ptr AnalysisSurfaceCorrelationAction::performRedo(ActionState::ptr _state){
130 return Action::success;
131}
132
133bool AnalysisSurfaceCorrelationAction::canUndo() {
134 return true;
135}
136
137bool AnalysisSurfaceCorrelationAction::shouldUndo() {
138 return true;
139}
140/** =========== end of function ====================== */
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