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),
  92               std::back_inserter(expectedSimilarityGradient));
  93     for (auto& x : expectedSimilarityGradient)
  94     {
  95         x /= comparedDensity.asConstView().mapping().required_span_size();
  96     }
  97
  98     FloatingPointTolerance tolerance(defaultFloatTolerance());
  99
 100     // Need this conversion to vector of float, because Pointwise requires size()
 101     // member function not provided by basic_mdspan
 102     const basic_mdspan<const float, dynamicExtents3D> gradient =
 103             measure.gradient(comparedDensity.asConstView());
 104     ArrayRef<const float> gradientView(gradient.data(),
 105                                        gradient.data() + gradient.mapping().required_span_size());
 106     EXPECT_THAT(expectedSimilarityGradient, Pointwise(FloatEq(tolerance), gradientView));
 107 }
 108
 109 TEST(DensitySimilarityTest, GradientThrowsIfDensitiesDontMatch)
 110 {
 111     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
 112     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::innerProduct,
 113                                      referenceDensity.asConstView());
 114
 115     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 5);
 116     EXPECT_THROW(measure.gradient(comparedDensity.asConstView()), RangeError);
 117 }
 118
 119 TEST(DensitySimilarityTest, SimilarityThrowsIfDensitiesDontMatch)
 120 {
 121     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
 122     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::innerProduct,
 123                                      referenceDensity.asConstView());
 124     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 5);
 125     EXPECT_THROW(measure.similarity(comparedDensity.asConstView()), RangeError);
 126 }
 127
 128 TEST(DensitySimilarityTest, CopiedMeasureInnerProductIsCorrect)
 129 {
 130     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
 131     std::iota(begin(referenceDensity), end(referenceDensity), 0);
 132
 133     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::innerProduct,
 134                                      referenceDensity.asConstView());
 135
 136     DensitySimilarityMeasure                            copiedMeasure = measure;
 137     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 3);
 138     std::iota(begin(comparedDensity), end(comparedDensity), -18);
 139
 140     // 0*(-18) + 1*(-17) .. + 26 * 8 / Number elements
 141     const float expectedSimilarity =
 142             -117.0 / comparedDensity.asConstView().mapping().required_span_size();
 143     EXPECT_FLOAT_EQ(expectedSimilarity, copiedMeasure.similarity(comparedDensity.asConstView()));
 144 }
 145
 146 TEST(DensitySimilarityTest, RelativeEntropyOfSameDensityIsZero)
 147 {
 148     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
 149     std::iota(begin(referenceDensity), end(referenceDensity), -2);
 150
 151     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::relativeEntropy,
 152                                      referenceDensity.asConstView());
 153
 154     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 3);
 155     std::iota(begin(comparedDensity), end(comparedDensity), -2);
 156
 157     const float expectedSimilarity = 0;
 158     EXPECT_REAL_EQ(expectedSimilarity, measure.similarity(comparedDensity.asConstView()));
 159 }
 160
 161
 162 TEST(DensitySimilarityTest, RelativeEntropyIsCorrect)
 163 {
 164     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
 165     std::iota(begin(referenceDensity), end(referenceDensity), -2);
 166
 167     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::relativeEntropy,
 168                                      referenceDensity.asConstView());
 169
 170     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 3);
 171     std::iota(begin(comparedDensity), end(comparedDensity), -1);
 172
 173     const real expectedSimilarity = 22.468290398724498791;
 174     EXPECT_REAL_EQ(expectedSimilarity, measure.similarity(comparedDensity.asConstView()));
 175 }
 176
 177 TEST(DensitySimilarityTest, RelativeEntropyGradientIsCorrect)
 178 {
 179     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
 180     std::iota(begin(referenceDensity), end(referenceDensity), -1);
 181
 182     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::relativeEntropy,
 183                                      referenceDensity.asConstView());
 184
 185     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 3);
 186     std::iota(begin(comparedDensity), end(comparedDensity), -2);
 187
 188     // Need this conversion to ArrayRef, because Pointwise requires size()
 189     // member function not provided by basic_mdspan
 190     const basic_mdspan<const float, dynamicExtents3D> gradient =
 191             measure.gradient(comparedDensity.asConstView());
 192     ArrayRef<const float> gradientView(gradient.data(),
 193                                        gradient.data() + gradient.mapping().required_span_size());
 194
 195     TestReferenceData    refData;
 196     TestReferenceChecker checker(refData.rootChecker());
 197     checker.setDefaultTolerance(defaultFloatTolerance());
 198     checker.checkSequence(gradientView.begin(), gradientView.end(), "relative-entropy-gradient");
 199 }
 200
 201 TEST(DensitySimilarityTest, CrossCorrelationIsOne)
 202 {
 203     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(100, 100, 100);
 204     std::iota(begin(referenceDensity), end(referenceDensity), 10000);
 205
 206     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::crossCorrelation,
 207                                      referenceDensity.asConstView());
 208
 209     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(100, 100, 100);
 210     std::iota(begin(comparedDensity), end(comparedDensity), -10000);
 211
 212     const real expectedSimilarity = 1;
 213     EXPECT_REAL_EQ(expectedSimilarity, measure.similarity(comparedDensity.asConstView()));
 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     EXPECT_REAL_EQ(expectedSimilarity, measure.similarity(comparedDensity.asConstView()));
 233 }
 234
 235 TEST(DensitySimilarityTest, CrossCorrelationGradientIsZeroWhenCorrelated)
 236 {
 237     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(30, 30, 30);
 238     std::iota(begin(referenceDensity), end(referenceDensity), -1);
 239
 240     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::crossCorrelation,
 241                                      referenceDensity.asConstView());
 242
 243     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(30, 30, 30);
 244     std::iota(begin(comparedDensity), end(comparedDensity), -2);
 245
 246     // Need this conversion to ArrayRef, because Pointwise requires size()
 247     // member function not provided by basic_mdspan
 248     const basic_mdspan<const float, dynamicExtents3D> gradient =
 249             measure.gradient(comparedDensity.asConstView());
 250     ArrayRef<const float> gradientView(gradient.data(),
 251                                        gradient.data() + gradient.mapping().required_span_size());
 252
 253     std::array<float, 27000> expectedSimilarityGradient = {};
 254
 255     EXPECT_THAT(expectedSimilarityGradient, Pointwise(FloatEq(defaultFloatTolerance()), gradientView));
 256 }
 257
 258 TEST(DensitySimilarityTest, CrossCorrelationGradientIsCorrect)
 259 {
 260     MultiDimArray<std::vector<float>, dynamicExtents3D> referenceDensity(3, 3, 3);
 261     std::iota(begin(referenceDensity), end(referenceDensity), -1);
 262
 263     DensitySimilarityMeasure measure(DensitySimilarityMeasureMethod::crossCorrelation,
 264                                      referenceDensity.asConstView());
 265
 266     MultiDimArray<std::vector<float>, dynamicExtents3D> comparedDensity(3, 3, 3);
 267     std::iota(begin(comparedDensity), end(comparedDensity), -2);
 268
 269     // some non-linear transformation, so that we break the correlation
 270     for (float& valueToCompare : comparedDensity)
 271     {
 272         valueToCompare *= valueToCompare;
 273     }
 274
 275     // Need this conversion to ArrayRef, because Pointwise requires size()
 276     // member function not provided by basic_mdspan
 277     const basic_mdspan<const float, dynamicExtents3D> gradient =
 278             measure.gradient(comparedDensity.asConstView());
 279     ArrayRef<const float> gradientView(gradient.data(),
 280                                        gradient.data() + gradient.mapping().required_span_size());
 281
 282     TestReferenceData    refData;
 283     TestReferenceChecker checker(refData.rootChecker());
 284     checker.setDefaultTolerance(defaultFloatTolerance());
 285     checker.checkSequence(gradientView.begin(), gradientView.end(), "cross-correlation-gradient");
 286 }
 287
 288 } // namespace test
 289
 290 } // namespace gmx