src/gromacs/trajectoryanalysis/tests/surfacearea.cpp

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  36 /*! \internal \file
  37  * \brief
  38  * Tests for the surface area calculation used by the `sasa` analysis module.
  39  *
  40  * \author Teemu Murtola <teemu.murtola@gmail.com>
  41  * \ingroup module_trajectoryanalysis
  42  */
  43 #include "gmxpre.h"
  44
  45 #include "gromacs/trajectoryanalysis/modules/surfacearea.h"
  46
  47 #include <cstdlib>
  48
  49 #include <gtest/gtest.h>
  50
  51 #include "gromacs/math/units.h"
  52 #include "gromacs/math/utilities.h"
  53 #include "gromacs/math/vec.h"
  54 #include "gromacs/pbcutil/pbc.h"
  55 #include "gromacs/random/threefry.h"
  56 #include "gromacs/random/uniformrealdistribution.h"
  57 #include "gromacs/utility/arrayref.h"
  58 #include "gromacs/utility/gmxassert.h"
  59 #include "gromacs/utility/smalloc.h"
  60
  61 #include "testutils/refdata.h"
  62 #include "testutils/testasserts.h"
  63
  64 namespace
  65 {
  66
  67 /********************************************************************
  68  * SurfaceAreaTest
  69  */
  70
  71 class SurfaceAreaTest : public ::testing::Test
  72 {
  73 public:
  74     SurfaceAreaTest() :
  75         box_(),
  76         rng_(12345),
  77         area_(0.0),
  78         volume_(0.0),
  79         atomArea_(nullptr),
  80         dotCount_(0),
  81         dots_(nullptr)
  82     {
  83     }
  84     ~SurfaceAreaTest() override
  85     {
  86         sfree(atomArea_);
  87         sfree(dots_);
  88     }
  89
  90     void addSphere(real x, real y, real z, real radius, bool bAddToIndex = true)
  91     {
  92         if (bAddToIndex)
  93         {
  94             index_.push_back(x_.size());
  95         }
  96         x_.emplace_back(x, y, z);
  97         radius_.push_back(radius);
  98     }
  99
 100     void generateRandomPosition(rvec x, real* radius)
 101     {
 102         rvec                               fx;
 103         gmx::UniformRealDistribution<real> dist;
 104
 105         fx[XX] = dist(rng_);
 106         fx[YY] = dist(rng_);
 107         fx[ZZ] = dist(rng_);
 108         mvmul(box_, fx, x);
 109         *radius = 1.5 * dist(rng_) + 0.5;
 110     }
 111
 112     void generateRandomPositions(int count)
 113     {
 114         x_.reserve(count);
 115         radius_.reserve(count);
 116         index_.reserve(count);
 117         for (int i = 0; i < count; ++i)
 118         {
 119             rvec x;
 120             real radius = 0;
 121             generateRandomPosition(x, &radius);
 122             addSphere(x[XX], x[YY], x[ZZ], radius);
 123         }
 124     }
 125     void translatePoints(real x, real y, real z)
 126     {
 127         for (size_t i = 0; i < x_.size(); ++i)
 128         {
 129             x_[i][XX] += x;
 130             x_[i][YY] += y;
 131             x_[i][ZZ] += z;
 132         }
 133     }
 134
 135     void calculate(int ndots, int flags, bool bPBC)
 136     {
 137         volume_ = 0.0;
 138         sfree(atomArea_);
 139         atomArea_ = nullptr;
 140         dotCount_ = 0;
 141         sfree(dots_);
 142         dots_ = nullptr;
 143         t_pbc pbc;
 144         if (bPBC)
 145         {
 146             set_pbc(&pbc, PbcType::Xyz, box_);
 147         }
 148         gmx::SurfaceAreaCalculator calculator;
 149         calculator.setDotCount(ndots);
 150         calculator.setRadii(radius_);
 151         calculator.calculate(as_rvec_array(x_.data()),
 152                              bPBC ? &pbc : nullptr,
 153                              index_.size(),
 154                              index_.data(),
 155                              flags,
 156                              &area_,
 157                              &volume_,
 158                              &atomArea_,
 159                              &dots_,
 160                              &dotCount_);
 161     }
 162     real resultArea() const { return area_; }
 163     real resultVolume() const { return volume_; }
 164     real atomArea(int index) const { return atomArea_[index]; }
 165
 166     void checkReference(gmx::test::TestReferenceChecker* checker, const char* id, bool checkDotCoordinates)
 167     {
 168         gmx::test::TestReferenceChecker compound(checker->checkCompound("SASA", id));
 169         compound.checkReal(area_, "Area");
 170         if (volume_ > 0.0)
 171         {
 172             compound.checkReal(volume_, "Volume");
 173         }
 174         if (atomArea_ != nullptr)
 175         {
 176             compound.checkSequenceArray(index_.size(), atomArea_, "AtomArea");
 177         }
 178         if (dots_ != nullptr)
 179         {
 180             if (checkDotCoordinates)
 181             {
 182                 // The algorithm may produce the dots in different order in
 183                 // single and double precision due to some internal
 184                 // sorting...
 185                 std::qsort(dots_, dotCount_, sizeof(rvec), &dotComparer);
 186                 compound.checkSequenceArray(3 * dotCount_, dots_, "Dots");
 187             }
 188             else
 189             {
 190                 compound.checkInteger(dotCount_, "DotCount");
 191             }
 192         }
 193     }
 194
 195     gmx::test::TestReferenceData data_;
 196     matrix                       box_;
 197
 198 private:
 199     static int dotComparer(const void* a, const void* b)
 200     {
 201         for (int d = DIM - 1; d >= 0; --d)
 202         {
 203             const real ad = reinterpret_cast<const real*>(a)[d];
 204             const real bd = reinterpret_cast<const real*>(b)[d];
 205             // A fudge factor is needed to get an ordering that is the same
 206             // in single and double precision, since the points are not
 207             // exactly on the same Z plane even though in exact arithmetic
 208             // they probably would be.
 209             if (ad < bd - 0.001)
 210             {
 211                 return -1;
 212             }
 213             else if (ad > bd + 0.001)
 214             {
 215                 return 1;
 216             }
 217         }
 218         return 0;
 219     }
 220
 221     gmx::DefaultRandomEngine rng_;
 222     std::vector<gmx::RVec>   x_;
 223     std::vector<real>        radius_;
 224     std::vector<int>         index_;
 225
 226     real  area_;
 227     real  volume_;
 228     real* atomArea_;
 229     int   dotCount_;
 230     real* dots_;
 231 };
 232
 233 TEST_F(SurfaceAreaTest, ComputesSinglePoint)
 234 {
 235     gmx::test::FloatingPointTolerance tolerance(gmx::test::defaultRealTolerance());
 236     addSphere(1, 1, 1, 1);
 237     ASSERT_NO_FATAL_FAILURE(calculate(24, FLAG_VOLUME | FLAG_ATOM_AREA, false));
 238     EXPECT_REAL_EQ_TOL(4 * M_PI, resultArea(), tolerance);
 239     EXPECT_REAL_EQ_TOL(4 * M_PI, atomArea(0), tolerance);
 240     EXPECT_REAL_EQ_TOL(4 * M_PI / 3, resultVolume(), tolerance);
 241 }
 242
 243 TEST_F(SurfaceAreaTest, ComputesTwoPoints)
 244 {
 245     gmx::test::FloatingPointTolerance tolerance(gmx::test::relativeToleranceAsFloatingPoint(1.0, 0.005));
 246     addSphere(1, 1, 1, 1);
 247     addSphere(2, 1, 1, 1);
 248     ASSERT_NO_FATAL_FAILURE(calculate(1000, FLAG_ATOM_AREA, false));
 249     EXPECT_REAL_EQ_TOL(2 * 2 * M_PI * 1.5, resultArea(), tolerance);
 250     EXPECT_REAL_EQ_TOL(2 * M_PI * 1.5, atomArea(0), tolerance);
 251     EXPECT_REAL_EQ_TOL(2 * M_PI * 1.5, atomArea(1), tolerance);
 252 }
 253
 254 TEST_F(SurfaceAreaTest, ComputesTwoPointsOfUnequalRadius)
 255 {
 256     gmx::test::FloatingPointTolerance tolerance(gmx::test::relativeToleranceAsFloatingPoint(1.0, 0.005));
 257     // Spheres of radius 1 and 2 with intersection at 1.5
 258     const real dist = 0.5 + sqrt(3.25);
 259     addSphere(1.0, 1.0, 1.0, 1);
 260     addSphere(1.0 + dist, 1.0, 1.0, 2);
 261     ASSERT_NO_FATAL_FAILURE(calculate(1000, FLAG_ATOM_AREA, false));
 262     EXPECT_REAL_EQ_TOL(2 * M_PI * (1.5 + (dist - 0.5 + 2) * 2), resultArea(), tolerance);
 263     EXPECT_REAL_EQ_TOL(2 * M_PI * 1.5, atomArea(0), tolerance);
 264     EXPECT_REAL_EQ_TOL(2 * M_PI * (dist - 0.5 + 2) * 2, atomArea(1), tolerance);
 265 }
 266
 267 TEST_F(SurfaceAreaTest, SurfacePoints12)
 268 {
 269     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 270     addSphere(0, 0, 0, 1);
 271     ASSERT_NO_FATAL_FAILURE(calculate(12, FLAG_DOTS, false));
 272     checkReference(&checker, "Surface", true);
 273 }
 274
 275 TEST_F(SurfaceAreaTest, SurfacePoints32)
 276 {
 277     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 278     addSphere(0, 0, 0, 1);
 279     ASSERT_NO_FATAL_FAILURE(calculate(32, FLAG_DOTS, false));
 280     checkReference(&checker, "Surface", true);
 281 }
 282
 283 TEST_F(SurfaceAreaTest, SurfacePoints42)
 284 {
 285     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 286     addSphere(0, 0, 0, 1);
 287     ASSERT_NO_FATAL_FAILURE(calculate(42, FLAG_DOTS, false));
 288     checkReference(&checker, "Surface", true);
 289 }
 290
 291 TEST_F(SurfaceAreaTest, SurfacePoints122)
 292 {
 293     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 294     addSphere(0, 0, 0, 1);
 295     ASSERT_NO_FATAL_FAILURE(calculate(122, FLAG_DOTS, false));
 296     checkReference(&checker, "Surface", true);
 297 }
 298
 299 TEST_F(SurfaceAreaTest, Computes100Points)
 300 {
 301     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 302     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 303     box_[XX][XX] = 10.0;
 304     box_[YY][YY] = 10.0;
 305     box_[ZZ][ZZ] = 10.0;
 306     generateRandomPositions(100);
 307     ASSERT_NO_FATAL_FAILURE(calculate(24, FLAG_VOLUME | FLAG_ATOM_AREA | FLAG_DOTS, false));
 308     checkReference(&checker, "100Points", false);
 309 }
 310
 311 TEST_F(SurfaceAreaTest, Computes100PointsWithRectangularPBC)
 312 {
 313     // TODO: It would be nice to check that this produces the same result as
 314     // without PBC, without duplicating the reference files.
 315     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 316     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 317     box_[XX][XX] = 10.0;
 318     box_[YY][YY] = 10.0;
 319     box_[ZZ][ZZ] = 10.0;
 320     generateRandomPositions(100);
 321     box_[XX][XX]    = 20.0;
 322     box_[YY][YY]    = 20.0;
 323     box_[ZZ][ZZ]    = 20.0;
 324     const int flags = FLAG_ATOM_AREA | FLAG_VOLUME | FLAG_DOTS;
 325     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 326     checkReference(&checker, "100Points", false);
 327
 328     translatePoints(15.0, 0, 0);
 329     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 330     checkReference(&checker, "100Points", false);
 331
 332     translatePoints(-15.0, 15.0, 0);
 333     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 334     checkReference(&checker, "100Points", false);
 335
 336     translatePoints(0, -15.0, 15.0);
 337     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 338     checkReference(&checker, "100Points", false);
 339 }
 340
 341 TEST_F(SurfaceAreaTest, Computes100PointsWithTriclinicPBC)
 342 {
 343     // TODO: It would be nice to check that this produces the same result as
 344     // without PBC, without duplicating the reference files.
 345     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 346     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 347     box_[XX][XX] = 10.0;
 348     box_[YY][YY] = 10.0;
 349     box_[ZZ][ZZ] = 10.0;
 350     generateRandomPositions(100);
 351     box_[XX][XX] = 20.0;
 352     box_[YY][XX] = 10.0;
 353     box_[YY][YY] = 10.0 * sqrt(3.0);
 354     box_[ZZ][XX] = 10.0;
 355     box_[ZZ][YY] = 10.0 * sqrt(1.0 / 3.0);
 356     box_[ZZ][ZZ] = 20.0 * sqrt(2.0 / 3.0);
 357
 358     const int flags = FLAG_ATOM_AREA | FLAG_VOLUME | FLAG_DOTS;
 359     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 360     checkReference(&checker, "100Points", false);
 361
 362     translatePoints(15.0, 0, 0);
 363     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 364     checkReference(&checker, "100Points", false);
 365
 366     translatePoints(-15.0, box_[YY][YY] - 5.0, 0);
 367     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 368     checkReference(&checker, "100Points", false);
 369
 370     translatePoints(0, -(box_[YY][YY] - 5.0), 15.0);
 371     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 372     checkReference(&checker, "100Points", false);
 373 }
 374
 375 } // namespace