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 | * MatrixContentUnitTest.cpp
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25 | *
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26 | * Created on: Jan 8, 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 | using namespace std;
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36 |
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37 | #include <cppunit/CompilerOutputter.h>
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38 | #include <cppunit/extensions/TestFactoryRegistry.h>
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39 | #include <cppunit/ui/text/TestRunner.h>
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40 |
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41 | #include <cmath>
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42 | #include <limits>
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43 |
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44 | // include headers that implement a archive in simple text format
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45 | #include <boost/archive/text_oarchive.hpp>
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46 | #include <boost/archive/text_iarchive.hpp>
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47 |
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48 | #include "MatrixContentUnitTest.hpp"
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49 |
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50 | #include "MatrixContent.hpp"
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51 | #include "VectorContent.hpp"
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52 |
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53 | #ifdef HAVE_TESTRUNNER
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54 | #include "UnitTestMain.hpp"
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55 | #endif /*HAVE_TESTRUNNER*/
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56 |
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57 | /********************************************** Test classes **************************************/
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58 |
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59 | const std::string matrixA = " 9.962848439806617e-01 5.950413028139907e-01 3.172650036465889e-01\n\
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60 | 2.070939109924951e-01 8.365712117773689e-01 3.980567886073226e-01\n\
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61 | 1.021600573071414e-01 8.061359922326598e-02 8.493537275043391e-01\n\
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62 | 6.955361514014282e-01 6.873206387346102e-02 2.649165458481005e-01";
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63 | const std::string vectorS = "1.630290761001098e+00 7.624807744374841e-01 6.374093742147465e-01";
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64 |
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65 | // Registers the fixture into the 'registry'
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66 | CPPUNIT_TEST_SUITE_REGISTRATION( MatrixContentTest );
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67 |
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68 |
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69 | void MatrixContentTest::setUp()
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70 | {
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71 | m = new MatrixContent(4,3);
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72 | };
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73 |
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74 | void MatrixContentTest::tearDown()
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75 | {
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76 | delete(m);
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77 | };
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78 |
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79 | /** Unit Test for accessing matrix elements.
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80 | *
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81 | */
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82 | void MatrixContentTest::AccessTest()
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83 | {
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84 | // check whether all elements are initially zero
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85 | for (int i=0;i<4;i++)
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86 | for (int j=0;j<3;j++)
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87 | CPPUNIT_ASSERT_EQUAL( 0., m->at(i,j) );
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88 |
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89 | // set
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90 | for (int i=0;i<4;i++)
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91 | for (int j=0;j<3;j++)
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92 | m->set(i,j, i*3+j );
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93 |
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94 | // and check
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95 | double *ptr = NULL;
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96 | for (int i=0;i<4;i++)
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97 | for (int j=0;j<3;j++) {
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98 | CPPUNIT_ASSERT_EQUAL( (double)(i*3+j), m->at(i,j) );
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99 | ptr = m->Pointer(i,j);
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100 | CPPUNIT_ASSERT_EQUAL( (double)(i*3+j), *ptr );
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101 | }
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102 |
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103 | // assignment
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104 | for (int i=0;i<4;i++)
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105 | for (int j=0;j<3;j++)
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106 | m->set(i,j, i*3+j );
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107 | MatrixContent *dest = new MatrixContent(4,3);
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108 | *dest = *m;
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109 | for (int i=0;i<4;i++)
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110 | for (int j=0;j<3;j++)
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111 | CPPUNIT_ASSERT_EQUAL( dest->at(i,j), m->at(i,j) );
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112 | delete(dest);
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113 |
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114 | // out of bounds
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115 | //CPPUNIT_ASSERT_EQUAL(0., v->at(5,2) );
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116 | //CPPUNIT_ASSERT_EQUAL(0., v->at(2,17) );
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117 | //CPPUNIT_ASSERT_EQUAL(0., v->at(1024,140040) );
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118 | //CPPUNIT_ASSERT_EQUAL(0., v->at(-1,0) );
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119 | //CPPUNIT_ASSERT_EQUAL(0., v->at(0,-1) );
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120 | //CPPUNIT_ASSERT_EQUAL(0., v->at(-1,-1) );
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121 | };
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122 |
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123 | /** Unit Test for initializating matrices.
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124 | *
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125 | */
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126 | void MatrixContentTest::InitializationTest()
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127 | {
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128 | // set zero
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129 | m->setZero();
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130 | for (int i=0;i<4;i++)
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131 | for (int j=0;j<3;j++)
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132 | CPPUNIT_ASSERT_EQUAL( 0., m->at(i,j) );
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133 |
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134 | // set all
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135 | m->setValue(1.5);
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136 | for (int i=0;i<4;i++)
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137 | for (int j=0;j<3;j++)
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138 | CPPUNIT_ASSERT_EQUAL( 1.5, m->at(i,j) );
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139 |
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140 | // set basis
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141 | m->setIdentity();
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142 | for (int i=0;i<4;i++)
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143 | for (int j=0;j<3;j++)
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144 | CPPUNIT_ASSERT_EQUAL( i == j ? 1. : 0. , m->at(i,j) );
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145 |
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146 | // set from array
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147 | double array[] = { 1., 0., 0.,
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148 | 0., 1., 0.,
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149 | 0., 0., 1.,
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150 | 0., 0., 0. };
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151 | m->setFromDoubleArray(array);
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152 | for (int i=0;i<4;i++)
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153 | for (int j=0;j<3;j++)
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154 | CPPUNIT_ASSERT_EQUAL( i == j ? 1. : 0. , m->at(i,j) );
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155 |
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156 | };
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157 |
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158 | /** Unit Test for copying matrices.
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159 | *
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160 | */
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161 | void MatrixContentTest::CopyTest()
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162 | {
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163 | // set basis
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164 | MatrixContent *dest = NULL;
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165 | for (int i=0;i<4;i++) {
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166 | m->setValue(i);
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167 | dest = new MatrixContent(m);
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168 | for (int j=0;j<3;j++)
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169 | CPPUNIT_ASSERT_EQUAL( m->at(i,j) , dest->at(i,j) );
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170 |
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171 | delete(dest);
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172 | }
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173 | };
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174 |
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175 | /** Unit Test for exchanging rows and columns.
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176 | *
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177 | */
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178 | void MatrixContentTest::ExchangeTest()
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179 | {
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180 | // set to 1,1,1,2, ...
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181 | for (int i=0;i<4;i++)
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182 | for (int j=0;j<3;j++)
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183 | m->set(i,j, i+1 );
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184 |
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185 | // swap such that nothing happens
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186 | CPPUNIT_ASSERT_EQUAL( true, m->SwapColumns(1,2) );
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187 | for (int i=0;i<4;i++)
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188 | for (int j=0;j<3;j++)
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189 | CPPUNIT_ASSERT_EQUAL( (double)i+1., m->at(i,j) );
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190 |
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191 | // swap two rows
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192 | CPPUNIT_ASSERT_EQUAL( true, m->SwapRows(1,2) );
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193 | for (int i=0;i<4;i++)
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194 | for (int j=0;j<3;j++)
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195 | switch (i) {
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196 | case 0:
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197 | CPPUNIT_ASSERT_EQUAL( 1., m->at(i,j) );
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198 | break;
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199 | case 1:
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200 | CPPUNIT_ASSERT_EQUAL( 3., m->at(i,j) );
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201 | break;
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202 | case 2:
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203 | CPPUNIT_ASSERT_EQUAL( 2., m->at(i,j) );
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204 | break;
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205 | case 3:
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206 | CPPUNIT_ASSERT_EQUAL( 4., m->at(i,j) );
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207 | break;
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208 | default:
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209 | CPPUNIT_ASSERT_EQUAL( -1., m->at(i,j) );
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210 | break;
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211 | }
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212 | // check that op is reversable
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213 | CPPUNIT_ASSERT_EQUAL( true, m->SwapRows(1,2) );
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214 | for (int i=0;i<4;i++)
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215 | for (int j=0;j<3;j++)
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216 | CPPUNIT_ASSERT_EQUAL( (double)i+1., m->at(i,j) );
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217 |
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218 | // set to 1,2,3,1, ...
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219 | for (int i=0;i<4;i++)
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220 | for (int j=0;j<3;j++)
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221 | m->set(i,j, j+1. );
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222 |
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223 | // swap such that nothing happens
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224 | CPPUNIT_ASSERT_EQUAL( true, m->SwapRows(0,2) );
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225 | for (int i=0;i<4;i++)
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226 | for (int j=0;j<3;j++)
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227 | CPPUNIT_ASSERT_EQUAL( (double)j+1., m->at(i,j) );
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228 |
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229 | // swap two columns
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230 | CPPUNIT_ASSERT_EQUAL( true, m->SwapColumns(0,2) );
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231 | for (int i=0;i<4;i++)
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232 | for (int j=0;j<3;j++)
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233 | switch (j) {
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234 | case 0:
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235 | CPPUNIT_ASSERT_EQUAL( 3., m->at(i,j) );
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236 | break;
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237 | case 1:
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238 | CPPUNIT_ASSERT_EQUAL( 2., m->at(i,j) );
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239 | break;
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240 | case 2:
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241 | CPPUNIT_ASSERT_EQUAL( 1., m->at(i,j) );
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242 | break;
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243 | default:
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244 | CPPUNIT_ASSERT_EQUAL( -1., m->at(i,j) );
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245 | break;
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246 | }
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247 | // check that op is reversable
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248 | CPPUNIT_ASSERT_EQUAL( true, m->SwapColumns(0,2) );
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249 | for (int i=0;i<4;i++)
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250 | for (int j=0;j<3;j++)
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251 | CPPUNIT_ASSERT_EQUAL( (double)j+1., m->at(i,j) );
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252 |
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253 |
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254 | // set to 1,2,3,4, ...
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255 | MatrixContent *n = new MatrixContent(3,4);
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256 | for (int i=0;i<4;i++)
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257 | for (int j=0;j<3;j++) {
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258 | m->set(i,j, 3*i+j+1 );
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259 | n->set(j,i, 3*i+j+1 );
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260 | }
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261 | // transpose
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262 | MatrixContent res = (*m).transposed();
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263 | CPPUNIT_ASSERT( *n == res );
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264 | // second transpose
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265 | MatrixContent res2 = res.transposed();
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266 | CPPUNIT_ASSERT( *m == res2 );
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267 | delete n;
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268 | };
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269 |
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270 | /** Unit Test for matrix properties.
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271 | *
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272 | */
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273 | void MatrixContentTest::PropertiesTest()
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274 | {
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275 | // is zero
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276 | m->setZero();
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277 | CPPUNIT_ASSERT_EQUAL( true, m->IsNull() );
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278 | CPPUNIT_ASSERT_EQUAL( false, m->IsPositive() );
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279 | CPPUNIT_ASSERT_EQUAL( false, m->IsNegative() );
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280 | CPPUNIT_ASSERT_EQUAL( true, m->IsNonNegative() );
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281 |
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282 | // is positive
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283 | m->setValue(0.5);
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284 | CPPUNIT_ASSERT_EQUAL( false, m->IsNull() );
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285 | CPPUNIT_ASSERT_EQUAL( true, m->IsPositive() );
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286 | CPPUNIT_ASSERT_EQUAL( false, m->IsNegative() );
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287 | CPPUNIT_ASSERT_EQUAL( true, m->IsNonNegative() );
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288 |
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289 | // is negative
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290 | m->setValue(-0.1);
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291 | CPPUNIT_ASSERT_EQUAL( false, m->IsNull() );
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292 | CPPUNIT_ASSERT_EQUAL( false, m->IsPositive() );
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293 | CPPUNIT_ASSERT_EQUAL( true, m->IsNegative() );
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294 | CPPUNIT_ASSERT_EQUAL( false, m->IsNonNegative() );
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295 |
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296 | // is positive definite
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297 | CPPUNIT_ASSERT_EQUAL( false, m->IsPositiveDefinite() );
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298 | };
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299 |
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300 |
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301 | /** Unit test for reading from and writing matrix to stream
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302 | *
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303 | */
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304 | void MatrixContentTest::ReadWriteTest()
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305 | {
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306 | // set up matrix
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307 | for (int i=0;i<4;i++)
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308 | for (int j=0;j<3;j++)
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309 | m->set(i,j, i*3+j );
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310 |
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311 | // write to stream
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312 | std::stringstream matrixstream;
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313 | m->write(matrixstream);
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314 |
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315 | // parse in dimensions and check
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316 | std::pair<size_t, size_t> matrixdimensions = MatrixContent::preparseMatrixDimensions(matrixstream);
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317 | CPPUNIT_ASSERT_EQUAL( (size_t)4, matrixdimensions.first );
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318 | CPPUNIT_ASSERT_EQUAL( (size_t)3, matrixdimensions.second );
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319 | // parse in matrix and check
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320 | MatrixContent* n = new MatrixContent(4,3, matrixstream);
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321 | CPPUNIT_ASSERT_EQUAL( *m, *n );
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322 |
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323 | // free matrix
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324 | delete n;
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325 | }
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326 |
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327 | /** Unit test for MatrixContent::performSingularValueDecomposition().
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328 | *
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329 | */
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330 | void MatrixContentTest::SVDTest()
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331 | {
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332 | // setup "A", U,S,V
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333 | std::stringstream Astream(matrixA);
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334 | std::stringstream Sstream(vectorS);
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335 | MatrixContent A(m->getRows(), m->getColumns(), Astream);
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336 | VectorContent S_expected(m->getColumns(), Sstream);
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337 | *m = A;
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338 |
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339 | // check SVD
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340 | VectorContent S(m->getColumns());
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341 | MatrixContent V(m->getColumns(), m->getColumns());
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342 | A.performSingularValueDecomposition(V,S);
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343 | MatrixContent S_diag(m->getColumns(), m->getColumns());
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344 | for (size_t index = 0; index < m->getColumns(); ++index)
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345 | S_diag.set(index, index, S[index]);
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346 | CPPUNIT_ASSERT_EQUAL(*m,A*S_diag*(V.transpose()));
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347 | for (size_t index = 0; index < m->getColumns(); ++index) {
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348 | //CPPUNIT_ASSERT_EQUAL(S_expected[index], S[index]);
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349 | CPPUNIT_ASSERT(fabs(S_expected[index] - S[index]) < numeric_limits<double>::epsilon()*10.);
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350 | }
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351 |
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352 | // set up right-hand side
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353 | VectorContent b(4);
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354 | b[0] = 1.;
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355 | b[1] = 0.;
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356 | b[2] = 0.;
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357 | b[3] = 0.;
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358 |
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359 | // SVD
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360 | VectorContent x_expected(3);
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361 | x_expected[0] = -0.00209169;
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362 | x_expected[1] = -0.325399;
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363 | x_expected[2] = 0.628004;
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364 | const VectorContent x_result(A.solveOverdeterminedLinearEquation(V,S,b));
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365 |
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366 | // check result
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367 | for (size_t index = 0; index < m->getColumns(); ++index) {
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368 | CPPUNIT_ASSERT(fabs(x_expected[index] - x_result[index]) < 1.e-6);
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369 | }
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370 | }
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371 |
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372 | /** Unit test for serialization
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373 | *
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374 | */
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375 | void MatrixContentTest::SerializationTest()
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376 | {
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377 | m->setZero();
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378 | int count=0;
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379 | for (size_t x = 0; x < 4 ; ++x)
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380 | for (size_t y = 0; y < 3 ; ++y)
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381 | m->at(x,y) = count++;
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382 | // write element to stream
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383 | std::stringstream stream;
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384 | boost::archive::text_oarchive oa(stream);
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385 | oa << m;
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386 |
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387 | //std::cout << "Contents of archive is " << stream.str() << std::endl;
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388 |
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389 | // create and open an archive for input
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390 | boost::archive::text_iarchive ia(stream);
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391 | // read class state from archive
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392 | MatrixContent *newm;
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393 |
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394 | ia >> newm;
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395 |
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396 | CPPUNIT_ASSERT (*m == *newm);
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397 | }
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