source: src/Analysis/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp@ 2affd1

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Last change on this file since 2affd1 was 2affd1, checked in by Frederik Heber <heber@…>, 9 years ago

Removed molecules_deprecated from World and unnecessary includes of MoleculeListClass and all insert/erase.

  • this goes along the lines of removing "remove me when we don't need MoleculeCistClass anymore".
  • Property mode set to 100644
File size: 8.7 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 * AnalysisCorrelationToSurfaceUnitTest.cpp
25 *
26 * Created on: Oct 13, 2009
27 * Author: heber
28 */
29
30// include config.h
31#ifdef HAVE_CONFIG_H
32#include <config.h>
33#endif
34
35using namespace std;
36
37#include <cppunit/CompilerOutputter.h>
38#include <cppunit/extensions/TestFactoryRegistry.h>
39#include <cppunit/ui/text/TestRunner.h>
40
41#include <cstring>
42
43#include "Analysis/analysis_correlation.hpp"
44#include "Atom/atom.hpp"
45#include "CodePatterns/Assert.hpp"
46#include "Descriptors/MoleculeDescriptor.hpp"
47#include "Element/element.hpp"
48#include "Element/periodentafel.hpp"
49#include "LinkedCell/linkedcell.hpp"
50#include "LinkedCell/PointCloudAdaptor.hpp"
51#include "molecule.hpp"
52#include "Tesselation/boundary.hpp"
53#include "Tesselation/tesselation.hpp"
54#include "World.hpp"
55
56#include "AnalysisCorrelationToSurfaceUnitTest.hpp"
57
58#ifdef HAVE_TESTRUNNER
59#include "UnitTestMain.hpp"
60#endif /*HAVE_TESTRUNNER*/
61
62/********************************************** Test classes **************************************/
63
64// Registers the fixture into the 'registry'
65CPPUNIT_TEST_SUITE_REGISTRATION( AnalysisCorrelationToSurfaceUnitTest );
66
67void AnalysisCorrelationToSurfaceUnitTest::setUp()
68{
69 ASSERT_DO(Assert::Throw);
70
71 setVerbosity(5);
72
73 atom *Walker = NULL;
74
75 // init private all pointers to zero
76 TestSurfaceMolecule = NULL;
77 surfacemap = NULL;
78 binmap = NULL;
79 Surface = NULL;
80 LC = NULL;
81
82 // prepare element list
83 hydrogen = World::getInstance().getPeriode()->FindElement(1);
84 CPPUNIT_ASSERT(hydrogen != NULL && "hydrogen element not found");
85 elements.clear();
86
87 // construct molecule (tetraeder of hydrogens) base
88 TestSurfaceMolecule = World::getInstance().createMolecule();
89
90 Walker = World::getInstance().createAtom();
91 Walker->setType(hydrogen);
92 Walker->setPosition(Vector(1., 0., 1. ));
93 TestSurfaceMolecule->AddAtom(Walker);
94
95 Walker = World::getInstance().createAtom();
96 Walker->setType(hydrogen);
97 Walker->setPosition(Vector(0., 1., 1. ));
98 TestSurfaceMolecule->AddAtom(Walker);
99
100 Walker = World::getInstance().createAtom();
101 Walker->setType(hydrogen);
102 Walker->setPosition(Vector(1., 1., 0. ));
103 TestSurfaceMolecule->AddAtom(Walker);
104
105 Walker = World::getInstance().createAtom();
106 Walker->setType(hydrogen);
107 Walker->setPosition(Vector(0., 0., 0. ));
108 TestSurfaceMolecule->AddAtom(Walker);
109
110 // check that TestMolecule was correctly constructed
111 CPPUNIT_ASSERT_EQUAL( TestSurfaceMolecule->getAtomCount(), 4 );
112
113 TestSurfaceMolecule->ActiveFlag = true;
114
115 // init tesselation and linked cell
116 Surface = new Tesselation;
117 PointCloudAdaptor<molecule> cloud(TestSurfaceMolecule, TestSurfaceMolecule->name);
118 LC = new LinkedCell_deprecated(cloud, 5.);
119 FindNonConvexBorder(TestSurfaceMolecule, Surface, (const LinkedCell_deprecated *&)LC, 2.5, NULL);
120
121 // add outer atoms
122 carbon = World::getInstance().getPeriode()->FindElement(6);
123 TestSurfaceMolecule = World::getInstance().createMolecule();
124 Walker = World::getInstance().createAtom();
125 Walker->setType(carbon);
126 Walker->setPosition(Vector(4., 0., 4. ));
127 TestSurfaceMolecule->AddAtom(Walker);
128
129 Walker = World::getInstance().createAtom();
130 Walker->setType(carbon);
131 Walker->setPosition(Vector(0., 4., 4. ));
132 TestSurfaceMolecule->AddAtom(Walker);
133
134 Walker = World::getInstance().createAtom();
135 Walker->setType(carbon);
136 Walker->setPosition(Vector(4., 4., 0. ));
137 TestSurfaceMolecule->AddAtom(Walker);
138
139 // add inner atoms
140 Walker = World::getInstance().createAtom();
141 Walker->setType(carbon);
142 Walker->setPosition(Vector(0.5, 0.5, 0.5 ));
143 TestSurfaceMolecule->AddAtom(Walker);
144
145 World::getInstance().selectAllMolecules(AllMolecules());
146 allMolecules = const_cast<const World &>(World::getInstance()).getSelectedMolecules();
147 CPPUNIT_ASSERT_EQUAL( (size_t) 2, allMolecules.size());
148
149 // init maps
150 surfacemap = NULL;
151 binmap = NULL;
152
153};
154
155
156void AnalysisCorrelationToSurfaceUnitTest::tearDown()
157{
158 if (surfacemap != NULL)
159 delete(surfacemap);
160 if (binmap != NULL)
161 delete(binmap);
162
163 delete(Surface);
164 // note that all the atoms are cleaned by TestMolecule
165 delete(LC);
166 World::purgeInstance();
167 logger::purgeInstance();
168};
169
170
171/** Checks whether setup() does the right thing.
172 */
173void AnalysisCorrelationToSurfaceUnitTest::SurfaceTest()
174{
175 CPPUNIT_ASSERT_EQUAL( 4, TestSurfaceMolecule->getAtomCount() );
176 CPPUNIT_ASSERT_EQUAL( (size_t)2, allMolecules.size() );
177 CPPUNIT_ASSERT_EQUAL( (size_t)4, Surface->PointsOnBoundary.size() );
178 CPPUNIT_ASSERT_EQUAL( (size_t)6, Surface->LinesOnBoundary.size() );
179 CPPUNIT_ASSERT_EQUAL( (size_t)4, Surface->TrianglesOnBoundary.size() );
180};
181
182void AnalysisCorrelationToSurfaceUnitTest::CorrelationToSurfaceTest()
183{
184 // do the pair correlation
185 elements.push_back(hydrogen);
186 surfacemap = CorrelationToSurface( allMolecules, elements, Surface, LC );
187// OutputCorrelationToSurface ( (ofstream *)&cout, surfacemap );
188 CPPUNIT_ASSERT( surfacemap != NULL );
189 CPPUNIT_ASSERT_EQUAL( (size_t)4, surfacemap->size() );
190};
191
192void AnalysisCorrelationToSurfaceUnitTest::CorrelationToSurfaceHydrogenBinNoRangeTest()
193{
194 BinPairMap::iterator tester;
195 elements.push_back(hydrogen);
196 surfacemap = CorrelationToSurface( allMolecules, elements, Surface, LC );
197 // put pair correlation into bins and check with no range
198// OutputCorrelationToSurface ( (ofstream *)&cout, surfacemap );
199 binmap = BinData( surfacemap, 0.5, 0., 0. );
200 CPPUNIT_ASSERT_EQUAL( (size_t)1, binmap->size() );
201 OutputCorrelationMap<BinPairMap> ( (ofstream *)&cout, binmap, OutputCorrelation_Header, OutputCorrelation_Value );
202 tester = binmap->begin();
203 CPPUNIT_ASSERT_EQUAL( 0., tester->first );
204 CPPUNIT_ASSERT_EQUAL( 4, tester->second );
205
206};
207
208void AnalysisCorrelationToSurfaceUnitTest::CorrelationToSurfaceHydrogenBinRangeTest()
209{
210 BinPairMap::iterator tester;
211 elements.push_back(hydrogen);
212 surfacemap = CorrelationToSurface( allMolecules, elements, Surface, LC );
213// OutputCorrelationToSurface ( (ofstream *)&cout, surfacemap );
214 // ... and check with [0., 2.] range
215 binmap = BinData( surfacemap, 0.5, 0., 2. );
216 CPPUNIT_ASSERT_EQUAL( (size_t)5, binmap->size() );
217// OutputCorrelation ( (ofstream *)&cout, binmap );
218 tester = binmap->begin();
219 CPPUNIT_ASSERT_EQUAL( 0., tester->first );
220 CPPUNIT_ASSERT_EQUAL( 4, tester->second );
221 tester = binmap->find(1.);
222 CPPUNIT_ASSERT_EQUAL( 1., tester->first );
223 CPPUNIT_ASSERT_EQUAL( 0, tester->second );
224
225};
226
227void AnalysisCorrelationToSurfaceUnitTest::CorrelationToSurfaceCarbonBinNoRangeTest()
228{
229 BinPairMap::iterator tester;
230 elements.push_back(carbon);
231 surfacemap = CorrelationToSurface( allMolecules, elements, Surface, LC );
232// OutputCorrelationToSurface ( (ofstream *)&cout, surfacemap );
233 // put pair correlation into bins and check with no range
234 binmap = BinData( surfacemap, 0.5, 0., 0. );
235 //OutputCorrelation ( (ofstream *)&cout, binmap );
236 CPPUNIT_ASSERT_EQUAL( (size_t)9, binmap->size() );
237 // inside point is first and must have negative value
238 tester = binmap->lower_bound(4.25-0.5); // start depends on the min value and
239 CPPUNIT_ASSERT( tester != binmap->end() );
240 CPPUNIT_ASSERT_EQUAL( 3, tester->second );
241 // inner point
242 tester = binmap->lower_bound(0.);
243 CPPUNIT_ASSERT( tester != binmap->end() );
244 CPPUNIT_ASSERT_EQUAL( 1, tester->second );
245};
246
247void AnalysisCorrelationToSurfaceUnitTest::CorrelationToSurfaceCarbonBinRangeTest()
248{
249 BinPairMap::iterator tester;
250 elements.push_back(carbon);
251 surfacemap = CorrelationToSurface( allMolecules, elements, Surface, LC );
252// OutputCorrelationToSurface ( (ofstream *)&cout, surfacemap );
253 // ... and check with [0., 2.] range
254 binmap = BinData( surfacemap, 0.5, -2., 4. );
255 //OutputCorrelation ( (ofstream *)&cout, binmap );
256 CPPUNIT_ASSERT_EQUAL( (size_t)13, binmap->size() );
257 // three outside points
258 tester = binmap->lower_bound(4.25-0.5);
259 CPPUNIT_ASSERT( tester != binmap->end() );
260 CPPUNIT_ASSERT_EQUAL( 3, tester->second );
261 // inner point
262 tester = binmap->lower_bound(0.);
263 CPPUNIT_ASSERT( tester != binmap->end() );
264 CPPUNIT_ASSERT_EQUAL( 1, tester->second );
265};
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