src/gromacs/math/tests/densityfit.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Tests density fitting routines.
  38  *
  39  * \author Christian Blau <blau@kth.se>
  40  * \ingroup module_math
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "gromacs/math/densityfit.h"
  45
  46 #include <numeric>
  47
  48 #include <gtest/gtest.h>
  49
  50 #include "gromacs/math/multidimarray.h"
  51
  52 #include "testutils/refdata.h"
  53 #include "testutils/testasserts.h"
  54 #include "testutils/testmatchers.h"
  55
  56 namespace gmx
  57 {
  58
  59 namespace test
  60 {
  61
  62 TEST(DensitySimilarityTest, InnerProductIsCorrect)
  63 {
  64     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
  65     std::iota(begin(referenceDensity), end(referenceDensity), 0);
  66
  67     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::innerProduct,
  68                                      referenceDensity.asConstView());
  69
  70     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 3);
  71     std::iota(begin(comparedDensity), end(comparedDensity), -18);
  72
  73     // 0*(-18) + 1*(-17) .. + 26 * 8 / Number elements
  74     const float expectedSimilarity =
  75             -117.0 / comparedDensity.asConstView().mapping().required_span_size();
  76     EXPECT_FLOAT_EQ(expectedSimilarity, measure.similarity(comparedDensity.asConstView()));
  77 }
  78
  79 TEST(DensitySimilarityTest, InnerProductGradientIsCorrect)
  80 {
  81     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
  82     std::iota(begin(referenceDensity), end(referenceDensity), 0);
  83
  84     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::innerProduct,
  85                                      referenceDensity.asConstView());
  86
  87     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 3);
  88     std::iota(begin(comparedDensity), end(comparedDensity), -18);
  89
  90     std::vector<float> expectedSimilarityGradient;
  91     std::copy(begin(referenceDensity), end(referenceDensity), std::back_inserter(expectedSimilarityGradient));
  92     for (auto& x : expectedSimilarityGradient)
  93     {
  94         x /= comparedDensity.asConstView().mapping().required_span_size();
  95     }
  96
  97     FloatingPointTolerance tolerance(defaultFloatTolerance());
  98
  99     // Need this conversion to vector of float, because Pointwise requires size()
 100     // member function not provided by basic_mdspan
 101     const basic_mdspan<const float, dynamicExtents3D> gradient =
 102             measure.gradient(comparedDensity.asConstView());
 103     ArrayRef<const float> gradientView(gradient.data(),
 104                                        gradient.data() + gradient.mapping().required_span_size());
 105     EXPECT_THAT(expectedSimilarityGradient, Pointwise(FloatEq(tolerance), gradientView));
 106 }
 107
 108 TEST(DensitySimilarityTest, GradientThrowsIfDensitiesDontMatch)
 109 {
 110     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
 111     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::innerProduct,
 112                                      referenceDensity.asConstView());
 113
 114     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 5);
 115     EXPECT_THROW(measure.gradient(comparedDensity.asConstView()), RangeError);
 116 }
 117
 118 TEST(DensitySimilarityTest, SimilarityThrowsIfDensitiesDontMatch)
 119 {
 120     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
 121     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::innerProduct,
 122                                      referenceDensity.asConstView());
 123     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 5);
 124     EXPECT_THROW(measure.similarity(comparedDensity.asConstView()), RangeError);
 125 }
 126
 127 TEST(DensitySimilarityTest, CopiedMeasureInnerProductIsCorrect)
 128 {
 129     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
 130     std::iota(begin(referenceDensity), end(referenceDensity), 0);
 131
 132     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::innerProduct,
 133                                      referenceDensity.asConstView());
 134
 135     DensitySimilarityMeasure                            copiedMeasure = measure;
 136     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 3);
 137     std::iota(begin(comparedDensity), end(comparedDensity), -18);
 138
 139     // 0*(-18) + 1*(-17) .. + 26 * 8 / Number elements
 140     const float expectedSimilarity =
 141             -117.0 / comparedDensity.asConstView().mapping().required_span_size();
 142     EXPECT_FLOAT_EQ(expectedSimilarity, copiedMeasure.similarity(comparedDensity.asConstView()));
 143 }
 144
 145 TEST(DensitySimilarityTest, RelativeEntropyOfSameDensityIsZero)
 146 {
 147     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
 148     std::iota(begin(referenceDensity), end(referenceDensity), -2);
 149
 150     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::relativeEntropy,
 151                                      referenceDensity.asConstView());
 152
 153     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 3);
 154     std::iota(begin(comparedDensity), end(comparedDensity), -2);
 155
 156     const float expectedSimilarity = 0;
 157     EXPECT_REAL_EQ(expectedSimilarity, measure.similarity(comparedDensity.asConstView()));
 158 }
 159
 160
 161 TEST(DensitySimilarityTest, RelativeEntropyIsCorrect)
 162 {
 163     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
 164     std::iota(begin(referenceDensity), end(referenceDensity), -2);
 165
 166     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::relativeEntropy,
 167                                      referenceDensity.asConstView());
 168
 169     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 3);
 170     std::iota(begin(comparedDensity), end(comparedDensity), -1);
 171
 172     const real expectedSimilarity = 22.468290398724498791;
 173     EXPECT_REAL_EQ(expectedSimilarity, measure.similarity(comparedDensity.asConstView()));
 174 }
 175
 176 TEST(DensitySimilarityTest, RelativeEntropyGradientIsCorrect)
 177 {
 178     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
 179     std::iota(begin(referenceDensity), end(referenceDensity), -1);
 180
 181     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::relativeEntropy,
 182                                      referenceDensity.asConstView());
 183
 184     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 3);
 185     std::iota(begin(comparedDensity), end(comparedDensity), -2);
 186
 187     // Need this conversion to ArrayRef, because Pointwise requires size()
 188     // member function not provided by basic_mdspan
 189     const basic_mdspan<const float, dynamicExtents3D> gradient =
 190             measure.gradient(comparedDensity.asConstView());
 191     ArrayRef<const float> gradientView(gradient.data(),
 192                                        gradient.data() + gradient.mapping().required_span_size());
 193
 194     TestReferenceData    refData;
 195     TestReferenceChecker checker(refData.rootChecker());
 196     checker.setDefaultTolerance(defaultFloatTolerance());
 197     checker.checkSequence(gradientView.begin(), gradientView.end(), "relative-entropy-gradient");
 198 }
 199
 200 TEST(DensitySimilarityTest, CrossCorrelationIsOne)
 201 {
 202     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(100, 100, 100);
 203     std::iota(begin(referenceDensity), end(referenceDensity), 10000);
 204
 205     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::crossCorrelation,
 206                                      referenceDensity.asConstView());
 207
 208     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(100, 100, 100);
 209     std::iota(begin(comparedDensity), end(comparedDensity), -10000);
 210
 211     const real             expectedSimilarity = 1;
 212     FloatingPointTolerance tolerance(relativeToleranceAsUlp(1.0, 100'000));
 213     EXPECT_REAL_EQ_TOL(expectedSimilarity, measure.similarity(comparedDensity.asConstView()), tolerance);
 214 }
 215
 216 TEST(DensitySimilarityTest, CrossCorrelationIsMinusOneWhenAntiCorrelated)
 217 {
 218     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(100, 100, 100);
 219     std::iota(begin(referenceDensity), end(referenceDensity), 10000);
 220     for (auto& referenceDensityValue : referenceDensity)
 221     {
 222         referenceDensityValue *= -1;
 223     }
 224
 225     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::crossCorrelation,
 226                                      referenceDensity.asConstView());
 227
 228     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(100, 100, 100);
 229     std::iota(begin(comparedDensity), end(comparedDensity), -10000);
 230
 231     const real             expectedSimilarity = -1;
 232     FloatingPointTolerance tolerance(relativeToleranceAsUlp(-1.0, 100'000));
 233     EXPECT_REAL_EQ_TOL(expectedSimilarity, measure.similarity(comparedDensity.asConstView()), tolerance);
 234 }
 235
 236 TEST(DensitySimilarityTest, CrossCorrelationGradientIsZeroWhenCorrelated)
 237 {
 238     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(30, 30, 30);
 239     std::iota(begin(referenceDensity), end(referenceDensity), -1);
 240
 241     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::crossCorrelation,
 242                                      referenceDensity.asConstView());
 243
 244     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(30, 30, 30);
 245     std::iota(begin(comparedDensity), end(comparedDensity), -2);
 246
 247     // Need this conversion to ArrayRef, because Pointwise requires size()
 248     // member function not provided by basic_mdspan
 249     const basic_mdspan<const float, dynamicExtents3D> gradient =
 250             measure.gradient(comparedDensity.asConstView());
 251     ArrayRef<const float> gradientView(gradient.data(),
 252                                        gradient.data() + gradient.mapping().required_span_size());
 253
 254     std::array<float, 27000> expectedSimilarityGradient = {};
 255
 256     EXPECT_THAT(expectedSimilarityGradient, Pointwise(FloatEq(defaultFloatTolerance()), gradientView));
 257 }
 258
 259 TEST(DensitySimilarityTest, CrossCorrelationGradientIsCorrect)
 260 {
 261     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
 262     std::iota(begin(referenceDensity), end(referenceDensity), -1);
 263
 264     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::crossCorrelation,
 265                                      referenceDensity.asConstView());
 266
 267     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 3);
 268     std::iota(begin(comparedDensity), end(comparedDensity), -2);
 269
 270     // some non-linear transformation, so that we break the correlation
 271     for (float& valueToCompare : comparedDensity)
 272     {
 273         valueToCompare *= valueToCompare;
 274     }
 275
 276     // Need this conversion to ArrayRef, because Pointwise requires size()
 277     // member function not provided by basic_mdspan
 278     const basic_mdspan<const float, dynamicExtents3D> gradient =
 279             measure.gradient(comparedDensity.asConstView());
 280     ArrayRef<const float> gradientView(gradient.data(),
 281                                        gradient.data() + gradient.mapping().required_span_size());
 282
 283     TestReferenceData    refData;
 284     TestReferenceChecker checker(refData.rootChecker());
 285     checker.setDefaultTolerance(defaultFloatTolerance());
 286     checker.checkSequence(gradientView.begin(), gradientView.end(), "cross-correlation-gradient");
 287 }
 288
 289 } // namespace test
 290
 291 } // namespace gmx